[English] 日本語
Yorodumi
- PDB-1o13: Crystal structure of a putative dinitrogenase iron-molybdenum cof... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1o13
TitleCrystal structure of a putative dinitrogenase iron-molybdenum cofactor (tm1816) from thermotoga maritima at 1.83 A resolution
Componentsprobable NifB protein
KeywordsBIOSYNTHETIC PROTEIN / Ribonuclease h-like motif fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homologyMTH1175 domain / Dinitrogenase iron-molybdenum cofactor biosynthesis domain / Dinitrogenase iron-molybdenum cofactor biosynthesis / Dinitrogenase iron-molybdenum cofactor biosynthesis superfamily / Dinitrogenase iron-molybdenum cofactor / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta / Dinitrogenase iron-molybdenum cofactor biosynthesis domain-containing protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.83 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of probable NifB protein that is involved in FeMo-Co biosynthesis TM1816 from Thermotoga maritima at 1.83 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jan 25, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: probable NifB protein


Theoretical massNumber of molelcules
Total (without water)15,2511
Polymers15,2511
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.57, 39.84, 85.77
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein probable NifB protein


Mass: 15250.700 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: involved in FeMo-Co biosynthesis / Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1816 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X2D6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.2 Å3/Da / Density % sol: 43.55 %
Crystal growTemperature: 293 K / pH: 4.2
Details: 0.1M phosphate-citrate 40%(v/v) PEG-600, pH 4.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 4.20

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97903, 0.91837, 0.97874
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2002
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979031
20.918371
30.978741
ReflectionResolution: 1.83→42.871 Å / Num. obs: 10393 / % possible obs: 100 % / Redundancy: 14.9 % / Biso Wilson estimate: 24.76 Å2 / Rsym value: 0.089 / Net I/σ(I): 22.3
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.945 / % possible all: 100

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
RESOLVEmodel building
SOLVEphasing
CNS1refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.83→42.87 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: THERE WAS NO DENSITY FOR THE FINAL 17 RESIDUES OF THE GENE SEQUENCE. WATERS WERE ADDED TO 3.0+ SIGMA PEAKS IN MFO-DFC MAPS IN APPROPRIATE H-BONDING POSITIONS USING THE CNS WATER_PICK AND WATER_DELETE SCRIPTS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 498 4.8 %RANDOM
Rwork0.207 ---
obs0.207 10351 99.9 %-
all-10351 --
Solvent computationSolvent model: BULK SOLVENT CORRECTION / Bsol: 0.46 Å2 / ksol: 243.35 e/Å3
Displacement parametersBiso mean: 26.9 Å2
Baniso -1Baniso -2Baniso -3
1--6.928 Å20 Å20 Å2
2---2.383 Å20 Å2
3---9.312 Å2
Refine analyzeLuzzati d res low obs: 43 Å
Refinement stepCycle: LAST / Resolution: 1.83→42.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms808 0 0 96 904
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.56
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4541.5
X-RAY DIFFRACTIONc_mcangle_it2.1022
X-RAY DIFFRACTIONc_scbond_it2.0552
X-RAY DIFFRACTIONc_scangle_it2.9142.5
LS refinement shellResolution: 1.83→1.9 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3684 63 5.6 %
Rwork0.287 1053 -

+
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