[English] 日本語
Yorodumi
- PDB-1y56: Crystal structure of L-proline dehydrogenase from P.horikoshii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1y56
TitleCrystal structure of L-proline dehydrogenase from P.horikoshii
Components
  • hypothetical protein PH1363Hypothesis
  • sarcosine oxidase
KeywordsOXIDOREDUCTASE / dehydrogenase / protein-protein complex
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / ATP binding
Similarity search - Function
2Fe-2S iron-sulphur cluster binding domain, sarcosine oxidase, alpha subunit, N-terminal domain / BFD-like [2Fe-2S]-binding domain / BFD-like [2Fe-2S]-binding domain superfamily / SoxA, A3 domain / 2Fe-2S iron-sulfur cluster binding domain, N-terminal / Sarcosine oxidase A3 domain / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 ...2Fe-2S iron-sulphur cluster binding domain, sarcosine oxidase, alpha subunit, N-terminal domain / BFD-like [2Fe-2S]-binding domain / BFD-like [2Fe-2S]-binding domain superfamily / SoxA, A3 domain / 2Fe-2S iron-sulfur cluster binding domain, N-terminal / Sarcosine oxidase A3 domain / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / 2Fe-2S iron-sulfur cluster binding domain / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Ubiquitin-like (UB roll) / Arc Repressor Mutant, subunit A / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / : / FLAVIN MONONUCLEOTIDE / Uncharacterized protein / 382aa long hypothetical sarcosine oxidase / 382aa long hypothetical sarcosine oxidase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.86 Å
AuthorsTsuge, H. / Kawakami, R. / Sakuraba, H. / Ago, H. / Miyano, M. / Aki, K. / Katunuma, N. / Ohshima, T.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of a novel FAD-, FMN-, and ATP-containing L-proline dehydrogenase complex from Pyrococcus horikoshii
Authors: Tsuge, H. / Kawakami, R. / Sakuraba, H. / Ago, H. / Miyano, M. / Aki, K. / Katunuma, N. / Ohshima, T.
History
DepositionDec 2, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein PH1363
B: sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,5349
Polymers98,3762
Non-polymers2,1587
Water3,711206
1
A: hypothetical protein PH1363
B: sarcosine oxidase
hetero molecules

A: hypothetical protein PH1363
B: sarcosine oxidase
hetero molecules

A: hypothetical protein PH1363
B: sarcosine oxidase
hetero molecules

A: hypothetical protein PH1363
B: sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)402,13636
Polymers393,5058
Non-polymers8,63128
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+2/31
crystal symmetry operation12_555x,x-y,-z+2/31
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-77 kcal/mol
Surface area31510 Å2
MethodPISA
3
A: hypothetical protein PH1363
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9766
Polymers55,6391
Non-polymers1,3375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
B: sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5583
Polymers42,7371
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)172.219, 172.219, 175.398
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsThe biological assembly is a octamer generated by tetramer of hetero-dimer

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein hypothetical protein PH1363 / Hypothesis / L-proline dehydrogenase alpha subunit


Mass: 55639.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus RIL(DE3) / References: UniProt: O59088, EC: 1.5.99.8
#2: Protein sarcosine oxidase / / L-proline dehydrogenase beta subunit


Mass: 42737.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus RIL(DE3)
References: UniProt: Q5R1N3, UniProt: O59089*PLUS, EC: 1.5.99.8

-
Non-polymers , 8 types, 213 molecules

#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID / CAPS (buffer)


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 3.8 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 10.5
Details: CAPS, NaH2PO4, K2HPO4, Li2SO4, pH 10.5, EVAPORATION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 4, 2003
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→48.41 Å / Num. all: 38014 / Num. obs: 37913 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.8→2.96 Å / % possible all: 93.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.86→19.85 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.906 / SU B: 11.745 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.908 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22557 1655 5.1 %RANDOM
Rwork0.1817 ---
obs0.18396 31021 100 %-
all-38014 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.551 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å21.04 Å20 Å2
2--2.08 Å20 Å2
3----3.12 Å2
Refinement stepCycle: LAST / Resolution: 2.86→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6805 0 136 206 7147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227089
X-RAY DIFFRACTIONr_bond_other_d0.270.025
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9959597
X-RAY DIFFRACTIONr_angle_other_deg21.127310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1375855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48123.916309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.509151256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8021546
X-RAY DIFFRACTIONr_chiral_restr0.120.21046
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025285
X-RAY DIFFRACTIONr_gen_planes_other0.0920.025
X-RAY DIFFRACTIONr_nbd_refined0.230.23645
X-RAY DIFFRACTIONr_nbd_other0.5020.212
X-RAY DIFFRACTIONr_nbtor_refined0.3220.24806
X-RAY DIFFRACTIONr_nbtor_other0.3180.27
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2352
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7111.54326
X-RAY DIFFRACTIONr_mcbond_other0.1151.55
X-RAY DIFFRACTIONr_mcangle_it0.92126854
X-RAY DIFFRACTIONr_scbond_it1.39633270
X-RAY DIFFRACTIONr_scangle_it2.3624.52743
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.864→2.936 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 95 -
Rwork0.239 1846 -
obs--100 %

+
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