[English] 日本語
Yorodumi
- PDB-9jev: Crystal structure of a cupin protein (tm1459) in zinc (Zn) substi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jev
TitleCrystal structure of a cupin protein (tm1459) in zinc (Zn) substituted form
ComponentsCupin type-2 domain-containing protein
KeywordsMETAL BINDING PROTEIN / Cupin
Function / homologyCupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / Cupin type-2 domain-containing protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsFujieda, N. / Ichihashi, H. / Kurisu, G. / Itoh, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JSPS KAKENHI 21H01954 Japan
CitationJournal: Chem Asian J / Year: 2025
Title: Unusual Self-Hydroxylation in 4-Histidine Tetrad-Supporting Nonheme Iron Center.
Authors: Fujieda, N. / Ishihama, K.I. / Ichihashi, H. / Yanagisawa, S. / Kurisu, G. / Itoh, S.
History
DepositionSep 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cupin type-2 domain-containing protein
B: Cupin type-2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0504
Polymers26,9192
Non-polymers1312
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-107 kcal/mol
Surface area10330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.598, 57.871, 74.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cupin type-2 domain-containing protein


Mass: 13459.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1459 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1H0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 25%(w/v) Jeffamine ED-2001, 0.1 M MES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.12→50 Å / Num. obs: 85007 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 21.76
Reflection shellResolution: 1.12→1.14 Å / Redundancy: 7 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.64 / Num. unique obs: 4227 / % possible all: 100

-
Processing

Software
NameClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
SHELXLrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WSD

5wsd


Resolution: 1.12→30 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1767 4251 5 %RANDOM
Rwork0.138 ---
all0.1388 ---
obs0.1388 84933 99.8 %-
Refinement stepCycle: LAST / Resolution: 1.12→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3723 0 2 342 4067
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0105
X-RAY DIFFRACTIONs_angle_d0.0248
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.4097
X-RAY DIFFRACTIONs_zero_chiral_vol0.0768
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.6639
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.0251
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.0444
X-RAY DIFFRACTIONs_approx_iso_adps0.1467
LS refinement shellResolution: 1.12→1.16 Å /
RfactorNum. reflection
Rwork0.211 8131

+
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