[English] 日本語
Yorodumi
- PDB-30sm: Crystal structure of a omega-Hydroxyacid Iron-containing Dehydrogenase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 30sm
TitleCrystal structure of a omega-Hydroxyacid Iron-containing Dehydrogenase
ComponentsCvir-Hbd2
KeywordsOXIDOREDUCTASE / NAD-binding protein / Fe-dependent omega-Hydroxyacid dehydrogenase
Function / homology(R,R)-2,3-BUTANEDIOL / : / GAMMA-BUTYROLACTONE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological species[Clostridium] viride (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsMartins, B.M. / Begic, T. / Pierik, A.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chembiochem / Year: 2026
Title: omega-Hydroxyacid Dehydrogenases from Clostridium viride Iron-containing Biocatalysts with Biotechnological Potential
Authors: Begic, T. / Hill, J. / Stitzel, J.L. / Knauer, L. / Schuenemann, V. / Raschle, M. / Martins, B.M. / Pierik, A.J.
History
DepositionMay 12, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cvir-Hbd2
B: Cvir-Hbd2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,02720
Polymers81,3052
Non-polymers2,72218
Water10,088560
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.660, 116.660, 120.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11B-825-

HOH

21B-843-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Cvir-Hbd2


Mass: 40652.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Clostridium] viride (bacteria) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 6 types, 578 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GBL / GAMMA-BUTYROLACTONE / DIHYDROFURAN-2(3H)-ONE


Mass: 86.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.08 M MgSO4, 0.02 M NaCl, 0.02 M MES, 10 % (w/v) PEG 1450, pH 6

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid N2 / Crystal support: Mini-kappa goniometer / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2025 / Details: Rh-coated focusing glass mirror
RadiationMonochromator: Si(111) double-crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.73→41.85 Å / Num. obs: 190957 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.997 / Rrim(I) all: 0.225 / Net I/σ(I): 11.12
Reflection shellResolution: 1.73→1.83 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 1.31 / Num. unique obs: 30832 / CC1/2: 0.248 / Rrim(I) all: 2.349 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→41.85 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1992 2099 1.1 %
Rwork0.1764 --
obs0.1766 190946 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5720 0 169 560 6449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076103
X-RAY DIFFRACTIONf_angle_d0.8738313
X-RAY DIFFRACTIONf_dihedral_angle_d16.192353
X-RAY DIFFRACTIONf_chiral_restr0.054957
X-RAY DIFFRACTIONf_plane_restr0.0071060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.770.35071390.318412598X-RAY DIFFRACTION100
1.77-1.810.29651400.305112532X-RAY DIFFRACTION100
1.81-1.860.29981380.286412587X-RAY DIFFRACTION100
1.86-1.920.26281400.269212621X-RAY DIFFRACTION100
1.92-1.980.27771420.243312614X-RAY DIFFRACTION100
1.98-2.050.29031390.224312591X-RAY DIFFRACTION100
2.05-2.130.22351390.204112535X-RAY DIFFRACTION100
2.13-2.230.19391380.188412614X-RAY DIFFRACTION100
2.23-2.350.20631400.177912595X-RAY DIFFRACTION100
2.35-2.490.23511390.174412631X-RAY DIFFRACTION100
2.49-2.690.18191410.167412536X-RAY DIFFRACTION100
2.69-2.960.2281380.166312603X-RAY DIFFRACTION100
2.96-3.390.17851420.147412569X-RAY DIFFRACTION100
3.39-4.260.13561410.128612611X-RAY DIFFRACTION100
4.27-41.850.15071430.137412610X-RAY DIFFRACTION100

+
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