[English] 日本語
Yorodumi
- PDB-4iq0: Crystal structure of oxidoreductase, Gfo/Idh/MocA family from Str... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4iq0
TitleCrystal structure of oxidoreductase, Gfo/Idh/MocA family from Streptococcus pneumoniae with reductive methylated Lysine
ComponentsOxidoreductase, Gfo/Idh/MocA family
KeywordsOXIDOREDUCTASE / structural genomics / Midwest Center for Structural Genomics / PSI-Biology / MCSG / Gfo/Idh/MocA family / reductive methylation
Function / homology
Function and homology information


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
: / Oxidoreductase, Gfo/Idh/MocA family / Oxidoreductase, Gfo/Idh/MocA family
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsChang, C. / Hatzos-Skintges, C. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of oxidoreductase, Gfo/Idh/MocA family from Streptococcus pneumoniae with reductive methylated Lysine
Authors: Chang, C. / Hatzos-Skintges, C. / Abdullah, J. / Joachimiak, A.
History
DepositionJan 10, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJan 23, 2013ID: 2HO3
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Oxidoreductase, Gfo/Idh/MocA family
B: Oxidoreductase, Gfo/Idh/MocA family
C: Oxidoreductase, Gfo/Idh/MocA family
D: Oxidoreductase, Gfo/Idh/MocA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,2709
Polymers148,0754
Non-polymers1955
Water16,286904
1
A: Oxidoreductase, Gfo/Idh/MocA family
C: Oxidoreductase, Gfo/Idh/MocA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0773
Polymers74,0372
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-10 kcal/mol
Surface area25810 Å2
MethodPISA
2
B: Oxidoreductase, Gfo/Idh/MocA family
D: Oxidoreductase, Gfo/Idh/MocA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1946
Polymers74,0372
Non-polymers1564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-12 kcal/mol
Surface area25950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.915, 152.386, 100.237
Angle α, β, γ (deg.)90.000, 103.120, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Oxidoreductase, Gfo/Idh/MocA family /


Mass: 37018.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: SP_1482 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q97PV8, UniProt: A0A0H2UR04*PLUS
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 904 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M TRIS, 1.26 M Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 91010 / Num. obs: 90011 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 25.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 7 / Num. unique all: 8840 / % possible all: 98.6

-
Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SBC-CollectCOLLECTdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
ARP/wARPmodel building
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→38.6 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.905 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1952 4514 5 %RANDOM
Rwork0.1455 ---
all0.1481 89975 --
obs0.1481 89975 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.34 Å2 / Biso mean: 17.5895 Å2 / Biso min: 4.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0 Å20.15 Å2
2---0.37 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2→38.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9753 0 5 904 10662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01910155
X-RAY DIFFRACTIONr_bond_other_d0.0010.029460
X-RAY DIFFRACTIONr_angle_refined_deg1.1111.93913812
X-RAY DIFFRACTIONr_angle_other_deg0.718321681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90351259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14124.794509
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.528151537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.461532
X-RAY DIFFRACTIONr_chiral_restr0.070.21522
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211827
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022547
X-RAY DIFFRACTIONr_rigid_bond_restr2.677319615
X-RAY DIFFRACTIONr_sphericity_free29.6725260
X-RAY DIFFRACTIONr_sphericity_bonded6.474520009
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 292 -
Rwork0.138 6100 -
all-6392 -
obs-6392 96.92 %

+
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