[English] 日本語
Yorodumi
- PDB-1vrq: Crystal Structure of Heterotetrameric Sarcosine Oxidase from Cory... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vrq
TitleCrystal Structure of Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with Folinic Acid
Components(Sarcosine oxidase ...) x 4
KeywordsOXIDOREDUCTASE / Heterotetrameric sarcosine oxidase / flavoenzyme
Function / homology
Function and homology information


sarcosine oxidase (5,10-methylenetetrahydrofolate-forming) / sarcosine catabolic process / sarcosine oxidase activity / tetrahydrofolate metabolic process / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Folate-binding fold / Folate-binding superfamily / Heterotetrameric sarcosine oxidase / Sarcosine oxidase, alpha subunit / Sarcosine oxidase subunit beta / Sarcosine oxidase, delta subunit, heterotetrameric / Sarcosine oxidase, gamma subunit, heterotetrameric / Sarcosine oxidase, gamma subunit / Sarcosine oxidase subunit delta superfamily / Sarcosine oxidase, delta subunit family ...Folate-binding fold / Folate-binding superfamily / Heterotetrameric sarcosine oxidase / Sarcosine oxidase, alpha subunit / Sarcosine oxidase subunit beta / Sarcosine oxidase, delta subunit, heterotetrameric / Sarcosine oxidase, gamma subunit, heterotetrameric / Sarcosine oxidase, gamma subunit / Sarcosine oxidase subunit delta superfamily / Sarcosine oxidase, delta subunit family / Sarcosine oxidase, gamma subunit family / SoxA, A3 domain / 2Fe-2S iron-sulfur cluster binding domain, N-terminal / Sarcosine oxidase A3 domain / FAD dependent oxidoreductase / Glycine cleavage T-protein, C-terminal barrel domain / Glycine cleavage T-protein C-terminal barrel domain / Glycine cleavage T-protein/YgfZ, C-terminal / Probable tRNA modification gtpase trme; domain 1 / Aminomethyltransferase-like / Aminomethyltransferase, folate-binding domain / Aminomethyltransferase folate-binding domain / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / Rhodanese-like domain / 2Fe-2S iron-sulfur cluster binding domain / Gyrase A; domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N,N-DIMETHYLGLYCINE / FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / Chem-FON / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Sarcosine oxidase subunit gamma / Sarcosine oxidase subunit alpha / Sarcosine oxidase subunit delta / Sarcosine oxidase subunit beta
Similarity search - Component
Biological speciesCorynebacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsIda, K. / Moriguchi, T. / Suzuki, H.
CitationJournal: BIOCHEM.BIOPHYS.RES.COMMUN. / Year: 2005
Title: Crystal structure of heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96
Authors: Ida, K. / Moriguchi, T. / Suzuki, H.
History
DepositionApr 27, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Sarcosine oxidase alpha subunit
B: Sarcosine oxidase beta subunit
C: Sarcosine oxidase gamma subunit
D: Sarcosine oxidase delta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,87323
Polymers180,0774
Non-polymers3,79619
Water20,5551141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23780 Å2
ΔGint-261 kcal/mol
Surface area54360 Å2
MethodPISA
2
A: Sarcosine oxidase alpha subunit
B: Sarcosine oxidase beta subunit
C: Sarcosine oxidase gamma subunit
D: Sarcosine oxidase delta subunit
hetero molecules

A: Sarcosine oxidase alpha subunit
B: Sarcosine oxidase beta subunit
C: Sarcosine oxidase gamma subunit
D: Sarcosine oxidase delta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,74746
Polymers360,1558
Non-polymers7,59238
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area50370 Å2
ΔGint-535 kcal/mol
Surface area105910 Å2
MethodPISA
3
A: Sarcosine oxidase alpha subunit
B: Sarcosine oxidase beta subunit
C: Sarcosine oxidase gamma subunit
D: Sarcosine oxidase delta subunit
hetero molecules

A: Sarcosine oxidase alpha subunit
B: Sarcosine oxidase beta subunit
C: Sarcosine oxidase gamma subunit
D: Sarcosine oxidase delta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,74746
Polymers360,1558
Non-polymers7,59238
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area49790 Å2
ΔGint-538 kcal/mol
Surface area106490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.4017, 199.4017, 197.3089
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-3340-

HOH

21A-3466-

HOH

31C-3507-

HOH

-
Components

-
Sarcosine oxidase ... , 4 types, 4 molecules ABCD

#1: Protein Sarcosine oxidase alpha subunit


Mass: 102850.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. (bacteria) / Strain: U-96 / Plasmid: pET31b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q50LF0, sarcosine oxidase (formaldehyde-forming)
#2: Protein Sarcosine oxidase beta subunit


Mass: 44048.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. (bacteria) / Strain: U-96 / Plasmid: pET31b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q50LF2, sarcosine oxidase (formaldehyde-forming)
#3: Protein Sarcosine oxidase gamma subunit


Mass: 21732.541 Da / Num. of mol.: 1 / Fragment: residues 1-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. (bacteria) / Strain: U-96 / Plasmid: pET31b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q50LE9, sarcosine oxidase (formaldehyde-forming)
#4: Protein Sarcosine oxidase delta subunit


Mass: 11445.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. (bacteria) / Strain: U-96 / Plasmid: pET31b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q50LF1, sarcosine oxidase (formaldehyde-forming)

-
Non-polymers , 8 types, 1160 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#7: Chemical ChemComp-FON / N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid / [6R]-5-FORMYL-5,6,7,8-TETRAHYDROFOLATE / 6R-FOLINIC ACID


Mass: 473.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N7O7
#8: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#9: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#10: Chemical ChemComp-DMG / N,N-DIMETHYLGLYCINE / DIMETHYLGLYCINE


Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2
#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1141 / 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: 3.1 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.1M Tris-HCl, 1.9M Ammonium sulfate, 10mM CuSO4, pH 8.5, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→99.5 Å / Num. obs: 116783 / % possible obs: 100 % / Redundancy: 14.4 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.085
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.312 / Num. unique all: 16862 / % possible all: 100

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→99.5 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.2241 11676 RANDOM
Rwork0.192 --
obs0.192 116661 -
Refinement stepCycle: LAST / Resolution: 2.2→99.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12504 0 235 1141 13880
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.786241
X-RAY DIFFRACTIONc_angle_deg1.54823
X-RAY DIFFRACTIONc_dihedral_angle_d24.08819
X-RAY DIFFRACTIONc_improper_angle_d0.78409

+
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