[English] 日本語
Yorodumi
- PDB-3k20: X-ray structure of oxidoreductase from corynebacterium diphtheria... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k20
TitleX-ray structure of oxidoreductase from corynebacterium diphtheriae,hexagonal crystal form. northeast structural genomics consortium target cdr100d
Componentsoxidoreductase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / CdR100D / Q6NGSI_CORDI
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Uncharacterised protein family, CE1759 / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsKuzin, A. / Lew, S. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. ...Kuzin, A. / Lew, S. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target CdR100D
Authors: Kuzin, A. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionSep 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8415
Polymers20,4571
Non-polymers3844
Water59433
1
A: oxidoreductase
hetero molecules

A: oxidoreductase
hetero molecules

A: oxidoreductase
hetero molecules

A: oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,36620
Polymers81,8294
Non-polymers1,53716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area11350 Å2
ΔGint-300 kcal/mol
Surface area27460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.839, 99.839, 137.309
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-218-

HOH

-
Components

#1: Protein oxidoreductase /


Mass: 20457.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: DIP1437 / Plasmid: pET 14-15C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q6NGS1
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 4.83 Å3/Da / Density % sol: 74.53 %
Crystal growpH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:2.2M ammonium sulfate, 0.1M sodium acetate, 3% ethanol, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97879 0.91837 0.97926
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 4, 2009
Details: Si(111). A SECOND SET OF Si(220) crystals is also available.
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978791
20.918371
30.979261
ReflectionResolution: 2.5→30 Å / Num. obs: 26206 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 19.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.9 / % possible all: 98.7

-
Processing

Software
NameVersionClassificationNB
PHENIX1.4_115refinement
PDB_EXTRACT3data extraction
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.51 Å / SU ML: 0.35 / Phase error: 25.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 730 5.03 %
Rwork0.229 --
obs0.23 15251 99.5 %
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.06 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 20 33 1381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091363
X-RAY DIFFRACTIONf_angle_d1.2751857
X-RAY DIFFRACTIONf_dihedral_angle_d18.021475
X-RAY DIFFRACTIONf_chiral_restr0.083233
X-RAY DIFFRACTIONf_plane_restr0.006231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4985-2.69130.28851400.31962662X-RAY DIFFRACTION99
2.6913-2.96190.29051510.28042683X-RAY DIFFRACTION100
2.9619-3.38990.331660.26792719X-RAY DIFFRACTION100
3.3899-4.26890.22641330.20282783X-RAY DIFFRACTION100
4.2689-29.50960.17941400.18622944X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 33.3447 Å / Origin y: 31.5544 Å / Origin z: 35.8693 Å
111213212223313233
T0.3291 Å20.0116 Å20.0262 Å2-0.1768 Å2-0.0045 Å2--0.2351 Å2
L0.6836 °2-0.6892 °20.3472 °2-0.8396 °2-0.0608 °2--0.7438 °2
S-0.1441 Å °0.0721 Å °0.0234 Å °0.1873 Å °0.0257 Å °0.0844 Å °0.1453 Å °0.0408 Å °-0 Å °
Refinement TLS groupSelection details: all

+
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