[English] 日本語
Yorodumi
- PDB-8cu5: Crystal Structure of Putative Cyclophilin B from Brugia malayi -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cu5
TitleCrystal Structure of Putative Cyclophilin B from Brugia malayi
ComponentsPeptidyl-prolyl cis-trans isomeraseProlyl isomerase
KeywordsISOMERASE / SSGCID / peptidyl-prolyl cis-trans isomerase / rotamase / structural genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesBrugia malayi (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Crystal Structure of Putative Cyclophilin B from Brugia malayi
Authors: DeBouver, N.D. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMay 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase
B: Peptidyl-prolyl cis-trans isomerase
C: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,29113
Polymers64,5343
Non-polymers75710
Water9,458525
1
A: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7945
Polymers21,5111
Non-polymers2824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6693
Polymers21,5111
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8285
Polymers21,5111
Non-polymers3164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.220, 137.220, 143.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-492-

HOH

21B-606-

HOH

-
Components

#1: Protein Peptidyl-prolyl cis-trans isomerase / Prolyl isomerase / PPIase


Mass: 21511.359 Da / Num. of mol.: 3 / Fragment: BrmaA.00538.a.B2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis)
Gene: SM7 / Plasmid: BrmaA.00538.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6YNZ2, peptidylprolyl isomerase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: [Target: BrmaA.00538.a.B2.PD38321 - 20.5 mg/mL] [Barcode: 302391h9] [Pin: eko9-16] [Crystallization: sparse screen - JCSG+ H9 -100 mM Bis-Tris pH 5.5, 200 mM Lithium sulfate, 25% (w/v) PEG ...Details: [Target: BrmaA.00538.a.B2.PD38321 - 20.5 mg/mL] [Barcode: 302391h9] [Pin: eko9-16] [Crystallization: sparse screen - JCSG+ H9 -100 mM Bis-Tris pH 5.5, 200 mM Lithium sulfate, 25% (w/v) PEG 3550, 14C, 0.4:0.4 drop ratio] [Cryo: 15% EG]

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 1, 2018 / Details: hybrid photon counting
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.85→48.51 Å / Num. obs: 58246 / % possible obs: 100 % / Redundancy: 9.503 % / Biso Wilson estimate: 27.75 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.046 / Χ2: 1.015 / Net I/σ(I): 31.91 / Num. measured all: 553484 / Scaling rejects: 168
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.99.480.6083.940108423242310.9310.643100
1.9-1.959.4160.4815.1939133416141560.9570.50999.9
1.95-2.019.4680.3516.6238211403740360.9770.371100
2.01-2.079.7460.2868.3838204392039200.9830.302100
2.07-2.149.7030.20411.3136938380938070.9910.21699.9
2.14-2.219.3980.1561434671369036890.9950.165100
2.21-2.299.4340.13617.1233435355035440.9960.14499.8
2.29-2.399.5910.11119.6432994344034400.9970.118100
2.39-2.499.7120.09223.3631983329332930.9980.097100
2.49-2.629.9060.07827.4331293315931590.9980.082100
2.62-2.769.5270.0635.0728648300730070.9990.063100
2.76-2.939.3430.04840.7126618284928490.9990.051100
2.93-3.139.5360.03851.71256152687268610.04100
3.13-3.389.5810.0364.56240002505250510.031100
3.38-3.79.5330.02577.45220872317231710.026100
3.7-4.148.9650.02380.62190062120212010.024100
4.14-4.789.3010.01992.06173841869186910.02100
4.78-5.859.6270.01990.23154131601160110.02100
5.85-8.279.0130.01888.84114291268126810.019100
8.27-48.518.430.01497.06631475774910.01598.9

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FRU

4fru


Resolution: 1.85→48.51 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1964 2023 3.48 %
Rwork0.1701 56192 -
obs0.1711 58215 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.05 Å2 / Biso mean: 35.5165 Å2 / Biso min: 17.73 Å2
Refinement stepCycle: final / Resolution: 1.85→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4236 0 44 533 4813
Biso mean--41.72 40.93 -
Num. residues----549
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.90.34151180.28439644082
1.9-1.950.26951210.246139984119
1.95-20.22111390.195839734112
2-2.070.21031340.172439724106
2.07-2.140.19631600.163439494109
2.14-2.230.22281250.17140114136
2.23-2.330.23421210.186539924113
2.33-2.450.22021360.192940134149
2.45-2.610.2171470.189439854132
2.61-2.810.24231590.185339984157
2.81-3.090.19951410.187140314172
3.09-3.540.18981840.160340074191
3.54-4.460.16571670.13440684235
4.46-48.510.1691710.158542314402
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.91954.2722-1.54817.5451-2.50742.35610.08720.00620.11120.17640.03860.15110.10010.055-0.16830.23360.0332-0.01390.205-0.04090.1079-19.9128-20.536125.3283
25.7414.12561.39854.3361.80172.6078-0.1068-0.0374-0.023-0.0869-0.08280.05330.14280.00290.1980.23010.0641-0.01370.1125-0.00080.1232-20.791-22.61320.6137
36.729-2.6865-1.03282.7677-0.16171.9403-0.1432-0.01220.2398-0.14160.0963-0.0502-0.03480.09410.03870.2321-0.0143-0.01660.17-0.03450.1547-21.3565-11.978316.0207
44.04773.2022-0.02222.9106-0.78843.021-0.48240.6140.2238-1.37680.41170.4937-0.31220.18550.07480.55330.0137-0.02540.31980.02210.2516-23.0635-17.58646.2469
52.3478-0.35510.30022.73280.01451.89390.01030.01070.0066-0.1608-0.10480.4010.0626-0.22390.08250.25230.0139-0.0360.2041-0.05220.2087-32.3676-17.875619.2455
62.4078-0.73470.8794.627-4.34295.285-0.1855-0.09340.35130.1548-0.0539-0.2114-0.29180.03590.20630.2790.0034-0.06670.2037-0.07310.3377-21.4244-2.292322.5068
72.92390.5477-0.1563.3754-1.02120.58730.0619-0.3264-0.18980.2734-0.0637-0.15060.02270.061-0.01460.32680.0015-0.04420.2451-0.04150.1121-20.7541-22.385427.2655
84.2751-1.9779-0.95843.5114.0426.1556-0.1009-0.0668-0.05150.2315-0.0530.38450.18230.05720.0990.1694-0.02210.01260.16750.03280.1771-8.4994-13.691838.7326
92.56661.80461.44735.78973.29513.73490.09150.01730.0149-0.0923-0.15660.0283-0.05210.02730.06070.19150.0068-0.02270.18320.04190.1886-2.8392-11.747338.6361
103.16352.3356-2.23767.4374-5.16554.87840.1471-0.0802-0.3351-0.0646-0.2805-0.31760.12590.34050.15730.1654-0.0182-0.04040.2239-0.01840.24761.5933-22.44339.4633
113.56172.27612.0696.32942.26864.25470.20260.1883-0.25480.00630.0224-1.09530.30570.3411-0.26990.19280.0307-0.01570.30750.05820.39611.392-16.924141.1517
122.00820.24770.2192.5313-0.14731.42370.0988-0.2876-0.12580.3245-0.1042-0.1706-0.00430.04310.00370.2132-0.0356-0.03740.22020.03290.2085-1.8952-16.359950.2256
134.7988-5.9730.5188.5007-1.68063.02280.06290.0338-0.2843-0.147-0.01550.11080.37060.007-0.04070.2627-0.0403-0.05760.2017-0.05580.3193-4.6596-31.79639.6957
142.4519-1.426-1.48994.72880.84843.68370.1129-0.01160.0153-0.1549-0.10840.2244-0.1457-0.1310.00050.0758-0.0386-0.08390.1823-0.03470.1802-9.341-12.09738.2596
152.33890.7979-1.38276.9216-1.41775.8779-0.2395-0.81520.8271-0.3344-0.06750.9250.0998-0.90880.32090.26710.0898-0.0160.7406-0.39130.6244-42.885313.481838.3291
163.3226-1.3988-0.00873.91131.15010.5131-0.111-1.12230.7875-0.0248-0.09290.2774-0.0532-0.23110.11430.33320.0577-0.03040.5501-0.29930.5074-37.790112.434741.1847
170.90650.6670.66285.10453.66766.6957-0.0591-0.31910.8116-0.3086-0.2220.0849-0.34720.01340.33590.20310.0441-0.05020.3136-0.16730.5274-32.994912.403230.175
182.1348-0.26210.58493.69163.56013.7648-0.10720.18061.5731-0.46310.3461-1.4483-0.63611.8553-0.03770.4289-0.07370.10630.7177-0.14440.7343-23.592612.826129.5108
195.9224.39180.06519.1345-3.89176.2793-0.4923-0.66220.1016-0.07630.2045-1.07450.1570.66850.31290.30110.0809-0.04150.585-0.19450.4824-23.58967.326441.5814
209.4744-1.92273.77265.68370.43065.94040.0185-1.004-0.20.4353-0.07530.32450.5736-0.57850.10440.3263-0.02770.05790.4696-0.1350.3059-38.9234-0.125738.3667
210.1677-0.1545-0.14163.82891.20073.7503-0.0051-0.48940.04530.2687-0.13790.25340.184-0.02540.12340.23910.03380.01380.3492-0.09990.3211-36.0912.170233.7514
226.9665-4.325-6.47517.16563.78829.14770.32240.48240.6156-0.6274-0.34440.1279-0.7456-0.84040.11040.39910.1007-0.15130.3243-0.10240.4543-38.916113.328220.5401
230.98760.1209-1.14464.13791.88282.6953-0.063-0.62840.8480.2967-0.15810.9078-0.1657-0.5920.1370.31010.086-0.01380.759-0.29580.7556-44.38413.144840.4166
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 38 )A21 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 65 )A39 - 65
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 88 )A66 - 88
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 108 )A89 - 108
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 159 )A109 - 159
6X-RAY DIFFRACTION6chain 'A' and (resid 160 through 180 )A160 - 180
7X-RAY DIFFRACTION7chain 'A' and (resid 181 through 203 )A181 - 203
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 38 )B21 - 38
9X-RAY DIFFRACTION9chain 'B' and (resid 39 through 65 )B39 - 65
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 88 )B66 - 88
11X-RAY DIFFRACTION11chain 'B' and (resid 89 through 108 )B89 - 108
12X-RAY DIFFRACTION12chain 'B' and (resid 109 through 159 )B109 - 159
13X-RAY DIFFRACTION13chain 'B' and (resid 160 through 180 )B160 - 180
14X-RAY DIFFRACTION14chain 'B' and (resid 181 through 203 )B181 - 203
15X-RAY DIFFRACTION15chain 'C' and (resid 21 through 38 )C21 - 38
16X-RAY DIFFRACTION16chain 'C' and (resid 39 through 65 )C39 - 65
17X-RAY DIFFRACTION17chain 'C' and (resid 66 through 88 )C66 - 88
18X-RAY DIFFRACTION18chain 'C' and (resid 89 through 98 )C89 - 98
19X-RAY DIFFRACTION19chain 'C' and (resid 99 through 108 )C99 - 108
20X-RAY DIFFRACTION20chain 'C' and (resid 109 through 124 )C109 - 124
21X-RAY DIFFRACTION21chain 'C' and (resid 125 through 159 )C125 - 159
22X-RAY DIFFRACTION22chain 'C' and (resid 160 through 180 )C160 - 180
23X-RAY DIFFRACTION23chain 'C' and (resid 181 through 203 )C181 - 203

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more