[English] 日本語
Yorodumi
- PDB-1vqs: Crystal structure of a nipsnap family protein with unknown functi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vqs
TitleCrystal structure of a nipsnap family protein with unknown function (atu4242) from agrobacterium tumefaciens str. c58 at 1.50 A resolution
Componentshypothetical protein AGR_L_1239Hypothesis
KeywordsUNKNOWN FUNCTION / Ferredoxin-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homologyAlpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesAgrobacterium tumefaciens str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (np_356412.1) from Agrobacterium tumefaciens at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein AGR_L_1239
B: hypothetical protein AGR_L_1239
C: hypothetical protein AGR_L_1239
D: hypothetical protein AGR_L_1239
E: hypothetical protein AGR_L_1239
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,12812
Polymers69,4115
Non-polymers7177
Water17,168953
1
A: hypothetical protein AGR_L_1239
B: hypothetical protein AGR_L_1239
hetero molecules

A: hypothetical protein AGR_L_1239
B: hypothetical protein AGR_L_1239
hetero molecules

A: hypothetical protein AGR_L_1239
B: hypothetical protein AGR_L_1239
hetero molecules

A: hypothetical protein AGR_L_1239
B: hypothetical protein AGR_L_1239
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,30020
Polymers111,0588
Non-polymers1,24112
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area25810 Å2
ΔGint-351 kcal/mol
Surface area33320 Å2
MethodPISA, PQS
2
C: hypothetical protein AGR_L_1239
D: hypothetical protein AGR_L_1239
hetero molecules

C: hypothetical protein AGR_L_1239
D: hypothetical protein AGR_L_1239
hetero molecules

C: hypothetical protein AGR_L_1239
D: hypothetical protein AGR_L_1239
hetero molecules

C: hypothetical protein AGR_L_1239
D: hypothetical protein AGR_L_1239
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,30020
Polymers111,0588
Non-polymers1,24112
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area24500 Å2
ΔGint-250 kcal/mol
Surface area33370 Å2
MethodPISA, PQS
3
E: hypothetical protein AGR_L_1239
hetero molecules
x 5


Theoretical massNumber of molelcules
Total (without water)69,89210
Polymers69,4115
Non-polymers4805
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_546x,-y-1,-z+11
crystal symmetry operation7_646y+1,x-1,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area21980 Å2
ΔGint-130 kcal/mol
Surface area34010 Å2
MethodPISA
4
E: hypothetical protein AGR_L_1239
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)111,82716
Polymers111,0588
Non-polymers7698
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_546x,-y-1,-z+11
crystal symmetry operation7_646y+1,x-1,-z+11
crystal symmetry operation8_556-y,-x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)94.792, 94.792, 303.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-105-

SO4

21B-105-

SO4

31C-105-

SO4

41D-105-

SO4

51E-105-

SO4

61B-178-

HOH

71B-297-

HOH

81B-298-

HOH

91C-270-

HOH

101C-275-

HOH

111D-258-

HOH

121D-288-

HOH

131E-214-

HOH

141E-218-

HOH

-
Components

#1: Protein
hypothetical protein AGR_L_1239 / Hypothesis


Mass: 13882.296 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. C58 (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / ATCC 33970 / Gene: np_356412.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U857
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 953 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 14% PEG MME 2000, 0.175M Sulfate_NH4, 0.05M Tris_base, 0.05M Tris Cl, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.3.110.979648
SYNCHROTRONALS 8.3.120.979648,1.019943
DetectorType: ADSC / Detector: CCD / Date: Oct 9, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)MADMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9796481
21.0199431
ReflectionResolution: 1.5→29.97 Å / Num. obs: 110198 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 23.19 Å2 / Rsym value: 0.09 / Net I/σ(I): 13.2
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 8036 / Rsym value: 0.59 / % possible all: 100

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALACCP4 4.2data scaling
SOLVEphasing
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→29.97 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.659 / SU ML: 0.032 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.063
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AMMONIUM SULFATE IS INCLUDED IN THE CRYSTALLIZATION AND FIVE PAIRS OF PARTIAL OCCUPANCY SULFATE ANIONS ARE LOCATED NEAR THE SIDECHAIN OF ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AMMONIUM SULFATE IS INCLUDED IN THE CRYSTALLIZATION AND FIVE PAIRS OF PARTIAL OCCUPANCY SULFATE ANIONS ARE LOCATED NEAR THE SIDECHAIN OF ARG 9 ON EACH SUBUNIT. THE SULATE MOLECULES IN EACH PAIR ARE RELATED BY A 4-FOLD INVERSION SYMMETRY AXIS THAT COINCIDES WITH THE CRYSTALLOGRAPHIC FOUR-FOLD AXIS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17681 5508 5 %RANDOM
Rwork0.15099 ---
obs0.1523 104690 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.154 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4563 0 41 953 5557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224865
X-RAY DIFFRACTIONr_bond_other_d0.0040.024501
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9666578
X-RAY DIFFRACTIONr_angle_other_deg0.886310432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.935560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.13322.134239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.03415876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.351548
X-RAY DIFFRACTIONr_chiral_restr0.090.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025272
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021066
X-RAY DIFFRACTIONr_nbd_refined0.2160.2806
X-RAY DIFFRACTIONr_nbd_other0.2070.24338
X-RAY DIFFRACTIONr_nbtor_other0.0820.22640
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2724
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.2252
X-RAY DIFFRACTIONr_symmetry_hbond_other0.2030.21
X-RAY DIFFRACTIONr_mcbond_it1.91733435
X-RAY DIFFRACTIONr_mcbond_other0.35731127
X-RAY DIFFRACTIONr_mcangle_it1.84354566
X-RAY DIFFRACTIONr_scbond_it3.50982307
X-RAY DIFFRACTIONr_scangle_it4.484112012
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22197
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 411 5.12 %
Rwork0.234 7613 -
obs--99.84 %
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)
10.4119-0.0610.01730.2259-0.00160.56090.00030.04360.1009-0.01830.0065-0.0417-0.09380.0172-0.0068-0.1164-0.01420.0153-0.13710.0084-0.113610.62717.49663.747
20.22140.00330.00660.4255-0.01630.99720.0265-0.0111-0.0217-0.00050.004-0.12990.04660.2202-0.0305-0.15270.0131-0.0104-0.0856-0.0185-0.109120.284-2.791117.183
31.2471-0.5462-0.32460.81410.03230.9031-0.00640.06140.1636-0.0229-0.07510.0626-0.2147-0.13150.0815-0.08960.0166-0.0526-0.14510.0059-0.094341.753-26.948142.892
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-5 - 1047 - 116
21BB-6 - 1046 - 116
32CC-5 - 1047 - 116
42DD-5 - 1047 - 116
53EE-5 - 1047 - 116

+
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