[English] 日本語
Yorodumi
- PDB-7twe: Crystal Structure of the Putative Oxidoreductase of DUF1479-conta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7twe
TitleCrystal Structure of the Putative Oxidoreductase of DUF1479-containing Protein Family YPO2976 from Yersinia pestis Bound to 2-oxo-glutaric acid
ComponentsDUF1479 domain-containing protein
KeywordsUNKNOWN FUNCTION / Uncharacterized protein / oxidoreductase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyGig2-like / Gig2-like / Isopenicillin N synthase-like superfamily / 2-OXOGLUTARIC ACID / : / DUF1479 domain-containing protein
Function and homology information
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsKim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Schneewind, O. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Putative Oxidoreductase of DUF1479-containing Protein Family YPO2976 from Yersinia pestis Bound to 2-oxo-glutaric acid
Authors: Kim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Schneewind, O. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DUF1479 domain-containing protein
B: DUF1479 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4967
Polymers95,0322
Non-polymers4645
Water1,56787
1
A: DUF1479 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7173
Polymers47,5161
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DUF1479 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7794
Polymers47,5161
Non-polymers2633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.426, 54.054, 148.290
Angle α, β, γ (deg.)90.000, 92.971, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein DUF1479 domain-containing protein


Mass: 47516.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Strain: CO92 / Gene: YPO2976 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): gold / References: UniProt: A0A3G5LE49
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium Chloride, 0.1 M TrisHCl pH 8.5, 25 % (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 32217 / % possible obs: 96 % / Redundancy: 2.9 % / Biso Wilson estimate: 35.75 Å2 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.076 / Rrim(I) all: 0.14 / Net I/σ(I): 9.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 1204 / CC1/2: 0.65 / Rpim(I) all: 0.355 / Rrim(I) all: 0.553 / % possible all: 72.6

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 4RGK

4rgk


Resolution: 2.41→38.33 Å / SU ML: 0.2821 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.2792
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2356 1409 5.09 %
Rwork0.1979 26267 -
obs0.1999 27676 81.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.17 Å2
Refinement stepCycle: LAST / Resolution: 2.41→38.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6425 0 26 87 6538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00166623
X-RAY DIFFRACTIONf_angle_d0.40928993
X-RAY DIFFRACTIONf_chiral_restr0.0401948
X-RAY DIFFRACTIONf_plane_restr0.00421210
X-RAY DIFFRACTIONf_dihedral_angle_d13.5462457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.490.3753580.27161149X-RAY DIFFRACTION35.74
2.49-2.590.2969790.25251767X-RAY DIFFRACTION54.97
2.59-2.710.30071020.25942079X-RAY DIFFRACTION65.18
2.71-2.850.30271360.24742439X-RAY DIFFRACTION76.64
2.85-3.030.28631560.24242829X-RAY DIFFRACTION88.73
3.03-3.270.26971620.2283106X-RAY DIFFRACTION98.05
3.27-3.590.25211850.19453207X-RAY DIFFRACTION99.71
3.59-4.110.20081650.17153199X-RAY DIFFRACTION99.67
4.11-5.180.21061630.16143226X-RAY DIFFRACTION99.65
5.18-38.330.19892030.18713266X-RAY DIFFRACTION98.55
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)
11.303729079890.469973485090.3272218170683.411323139962.028731024812.90450482799-0.1554470946360.243858584648-0.2289299137140.238110381415-0.2982704924490.3795194671720.764344966456-0.8018919531010.4392202164870.374916205832-0.119133187495-0.009671295871680.248589498477-0.005807728604150.173258124616-3.78261339079-11.874857092348.7767461268
22.5775449938-0.0375645059619-0.7028532436991.650519939970.3118829687363.479028736650.000943771681454-0.5787762995450.3715950485090.2294690527550.173611863208-0.125641318601-0.04033564646540.387612332939-0.1403049524440.2439471061090.0892272406954-0.05559159974340.363233838921-0.1464545609190.25421554085914.89485340425.26230823265.3603320325
32.40071969029-0.447523844038-0.159248663972.362831790481.591301508763.55131799644-0.0924356916529-0.02273533368510.02836274829430.04342738510740.100133104138-0.09542071895190.396930562407-0.0997368323153-0.009526500567160.227238234657-0.02961226838230.007276894309060.200744395723-0.01304589106290.132326856734.59535828939-3.1206365617853.4612108629
43.26331550721-0.08393809216220.2512697743551.60968177944-0.4977802055133.554092983650.0834035774811-0.4016994760920.275456700611-0.3781308751880.08706416198510.00769410018550.112161728440.433635186792-0.1349874520980.1729967513750.0389154021512-0.06789443465580.387191773873-0.1735709773560.2784432184218.53469196345.0535701057159.6907390099
52.556134241661.816218861371.417072023722.46535430991.217994119464.39136422986-0.329915055239-0.5294414820390.3217869646280.07716452624110.234827536584-0.709549631504-0.2575891358420.9044699039110.09294570281760.1971743832650.0900116794427-0.0589435640920.649953119835-0.3010136433880.52014625253930.48753268376.9630202275661.4366799897
61.83665819297-0.0774848197506-0.08574004674942.806484889341.196596937482.704691164510.0480632775883-0.01576736202710.602473032010.2341418441030.002500616581170.548960997732-0.56326267358-0.761657335980.2177117621450.4074806504340.1233376742160.1487884848520.160104785862-0.001557821136250.395706249306-0.1021390412435.5998815084924.5103336031
73.280564465060.67159820013-0.7700497259370.7276326672390.4023797838332.16967093883-0.1068616936310.950453945842-0.52941709577-0.107930765605-0.0106413762871-0.07209335487720.141663768766-0.0680146043092-0.007594077725030.202939446564-0.05901892256140.03429263717330.49536485392-0.161426838690.30327588027918.7715527559-15.45573010477.59299095114
83.36727846904-0.515873125257-0.1504634041830.9990798349890.2741482425332.693699775660.04961962241770.4031021052710.4225223748340.0589756934878-0.0123058065165-0.210110618857-0.4886161407630.0665096793017-0.07018945580540.261577365948-0.02465220326970.06184231757150.2224667424770.03920055922260.27320557456215.64074305050.70807122441717.8713659073
93.56992588121-0.832669695704-0.6537170723091.609835739120.2241788219682.24039437963-0.04554782255950.285093494437-0.1369419065170.1527783340460.00945438098989-0.0190080075081-0.02634001463750.007126500534340.02091084179490.180765497392-0.06916449325720.02852514250190.204190668117-0.03522461192170.16371151266616.5946467625-9.7482187149618.4567455537
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 52 )AA3 - 521 - 50
22chain 'A' and (resid 53 through 185 )AA53 - 18551 - 178
33chain 'A' and (resid 186 through 342 )AA186 - 342179 - 335
44chain 'A' and (resid 343 through 379 )AA343 - 379336 - 372
55chain 'A' and (resid 380 through 416 )AA380 - 416373 - 409
66chain 'B' and (resid 5 through 52 )BD5 - 521 - 48
77chain 'B' and (resid 53 through 162 )BD53 - 16249 - 142
88chain 'B' and (resid 163 through 259 )BD163 - 259143 - 239
99chain 'B' and (resid 260 through 415 )BD260 - 415240 - 395

+
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