[English] 日本語
Yorodumi
- PDB-1tlt: Crystal Structure of a Putative Oxidoreductase (VIRULENCE FACTOR ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tlt
TitleCrystal Structure of a Putative Oxidoreductase (VIRULENCE FACTOR mviM HOMOLOG)
ComponentsPUTATIVE OXIDOREDUCTASE (VIRULENCE FACTOR mviM HOMOLOG)
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / NYSGXRC / T1535 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity
Similarity search - Function
Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative oxidoreductase YceM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsRajashankar, K.R. / Solorzano, V. / Kniewel, R. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of a Putative Oxidoreductase (VIRULENCE FACTOR mviM HOMOLOG)
Authors: RAJASHANKAR, K.R. / SOLORZANO, V. / KNIEWEL, R. / LIMA, C.D.
History
DepositionJun 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details ..._audit_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PUTATIVE OXIDOREDUCTASE (VIRULENCE FACTOR mviM HOMOLOG)
B: PUTATIVE OXIDOREDUCTASE (VIRULENCE FACTOR mviM HOMOLOG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,93610
Polymers70,1682
Non-polymers7698
Water64936
1
A: PUTATIVE OXIDOREDUCTASE (VIRULENCE FACTOR mviM HOMOLOG)
B: PUTATIVE OXIDOREDUCTASE (VIRULENCE FACTOR mviM HOMOLOG)
hetero molecules

A: PUTATIVE OXIDOREDUCTASE (VIRULENCE FACTOR mviM HOMOLOG)
B: PUTATIVE OXIDOREDUCTASE (VIRULENCE FACTOR mviM HOMOLOG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,87320
Polymers140,3364
Non-polymers1,53716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_546x,x-y-1,-z+7/61
Buried area12690 Å2
ΔGint-247 kcal/mol
Surface area46340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.856, 96.856, 380.817
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsFrom similarity to pdb entry 1OFG and from packing it is infered that the biological unit is a tetramer. The second part of the biological assembly can be generated by symmetry operation x,x-y-1,-z+7/6

-
Components

#1: Protein PUTATIVE OXIDOREDUCTASE (VIRULENCE FACTOR mviM HOMOLOG)


Mass: 35083.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MVIM, B1068 / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3 / References: UniProt: P75931
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.68 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.4M Ammonium Sulfate, 0.1M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 31-ID10.98
SYNCHROTRONNSLS X4A21.25
Detector
TypeIDDetectorDate
MARRESEARCH1CCDFeb 20, 2004
ADSC QUANTUM 42CCDFeb 13, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DiamondSINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
21.251
ReflectionResolution: 2.7→30 Å / Num. all: 29879 / Num. obs: 29879 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.31 % / Biso Wilson estimate: 46 Å2 / Rsym value: 0.119 / Net I/σ(I): 25.75
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 3.47 / Num. unique all: 2894 / Rsym value: 0.506 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD
Starting model: Experimental electron density.

Resolution: 2.7→19.91 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 196115.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Anomalous signal from a Ta6Br12 clusters was used to phase the structure
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1473 4.9 %RANDOM
Rwork0.245 ---
obs0.245 29801 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.7152 Å2 / ksol: 0.299474 e/Å3
Displacement parametersBiso mean: 50.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.76 Å29.55 Å20 Å2
2--2.76 Å20 Å2
3----5.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4691 0 40 36 4767
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 240 5.2 %
Rwork0.351 4337 -
obs--93.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

+
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