[English] 日本語
Yorodumi
- PDB-9zdi: Crystal structure of Zn-substituted Rubredoxin from hyperthermoph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9zdi
TitleCrystal structure of Zn-substituted Rubredoxin from hyperthermophilic bacterium Thermotoga maritima MSB8
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / rubredoxin / electron transfer / hyperthermophilic
Function / homology
Function and homology information


alkane catabolic process / electron transfer activity / iron ion binding
Similarity search - Function
Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile.
Similarity search - Domain/homology
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.02 Å
AuthorsDoukov, T.I. / George, D. / Jenney, F.E. / Cramer, S.P.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 2149122 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM65440 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133894 United States
CitationJournal: Biomolecules / Year: 2026
Title: Crystallography of Extremophile Proteins-Structural Comparisons of Psychrophilic and Hyperthermophilic Rubredoxins
Authors: Doukov, T. / Turpin, T.F. / George, D. / Cole, C. / Drumright, K. / Rumley, M. / Boyce, R. / Jenney, F.E. / Cramer, S.P.
History
DepositionNov 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rubredoxin
B: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1104
Polymers11,9792
Non-polymers1312
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.018, 50.030, 33.930
Angle α, β, γ (deg.)90.00, 110.80, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Rubredoxin


Mass: 5989.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: TM_0659
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9WZC7
#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.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: VAPOR DIFFUSION AGAINST 4.0M Ammonium Sulfate, pH 8.5,

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostat / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.77488 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2024
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77488 Å / Relative weight: 1
ReflectionResolution: 1.02→25.27 Å / Num. obs: 34060 / % possible obs: 88 % / Redundancy: 6.1 % / Biso Wilson estimate: 14.447 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.089 / Net I/σ(I): 6.2
Reflection shellResolution: 1.02→1.078 Å / Redundancy: 6.1 % / Rmerge(I) obs: 3.137 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1703 / CC1/2: 0.341 / Rpim(I) all: 1.427 / % possible all: 50.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.02→25.27 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.249 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18134 1611 4.7 %RANDOM
Rwork0.15191 ---
obs0.15324 32449 79.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.862 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20.42 Å2
2--0.53 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.02→25.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms820 0 0 108 928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.012897
X-RAY DIFFRACTIONr_bond_other_d0.0010.016789
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.8551229
X-RAY DIFFRACTIONr_angle_other_deg0.691.7921864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6125116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.22354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86910142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021051
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02173
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3361.122428
X-RAY DIFFRACTIONr_mcbond_other3.3231.12428
X-RAY DIFFRACTIONr_mcangle_it4.7332.522535
X-RAY DIFFRACTIONr_mcangle_other4.7462.525536
X-RAY DIFFRACTIONr_scbond_it5.4241.515469
X-RAY DIFFRACTIONr_scbond_other5.4191.516470
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1583.241688
X-RAY DIFFRACTIONr_long_range_B_refined10.3510.511042
X-RAY DIFFRACTIONr_long_range_B_other9.9539.861022
X-RAY DIFFRACTIONr_rigid_bond_restr4.24331686
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.02→1.045 Å
RfactorNum. reflection% reflection
Rfree0.318 20 -
Rwork0.266 363 -
obs--12.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.24510.67290.37751.9087-0.34741.74930.03290.0318-0.2263-0.0520.018-0.02580.17180.0022-0.05080.03090.0014-0.01190.0127-0.00650.021-6.55.85913.378
21.48710.61210.16193.5767-0.92433.6248-0.07110.0299-0.1173-0.2095-0.0217-0.09450.1368-0.03760.09280.0364-0.00470.01390.00380.00030.02553.57110.459-0.704
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 52
2X-RAY DIFFRACTION1A101
3X-RAY DIFFRACTION2B1 - 52
4X-RAY DIFFRACTION2B101

+
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