[English] 日本語
Yorodumi
- PDB-4gh5: Crystal structure of S-2-hydroxypropyl coenzyme M dehydrogenase (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gh5
TitleCrystal structure of S-2-hydroxypropyl coenzyme M dehydrogenase (S-HPCDH)
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / Rossmann Fold
Function / homology
Function and homology information


2-(S)-hydroxypropyl-CoM dehydrogenase / oxidoreductase activity / nucleotide binding
Similarity search - Function
PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2-(S)-hydroxypropyl-CoM dehydrogenase 3
Similarity search - Component
Biological speciesXanthobacter autotrophicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBakelar, J.W. / Johnson, S.J.
CitationJournal: Arch.Biochem.Biophys. / Year: 2013
Title: Crystal structures of S-HPCDH reveal determinants of stereospecificity for R- and S-hydroxypropyl-coenzyme M dehydrogenases.
Authors: Bakelar, J.W. / Sliwa, D.A. / Johnson, S.J.
History
DepositionAug 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
C: Short-chain dehydrogenase/reductase SDR
D: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,34112
Polymers108,4514
Non-polymers2,8908
Water18,5011027
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17630 Å2
ΔGint-126 kcal/mol
Surface area30030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.071, 127.921, 58.451
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-535-

HOH

21A-555-

HOH

31B-521-

HOH

41D-648-

HOH

-
Components

#1: Protein
Short-chain dehydrogenase/reductase SDR


Mass: 27112.775 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / Strain: Py2 / Gene: Xaut_5073 / Plasmid: pET28-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7IQH5
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1027 / 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 Å3/Da / Density % sol: 38.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.35M ammonium acetate, 27% polyethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 2, 2010 / Details: mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→35 Å / Num. all: 113574 / Num. obs: 113574 / % possible obs: 16 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.063 / Rsym value: 0.046 / Net I/σ(I): 25.75
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 1.92 / Num. unique all: 9812 / Rsym value: 0.423 / % possible all: 86

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CFC

2cfc


Resolution: 1.6→26.425 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1986 5687 5.01 %RANDOM
Rwork0.1708 ---
all0.1722 113447 --
obs0.1722 113447 98.22 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.254 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 13.77 Å2
Baniso -1Baniso -2Baniso -3
1--1.1666 Å2-0 Å2-0 Å2
2--0.2878 Å20 Å2
3---0.8788 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6895 0 192 1027 8114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067168
X-RAY DIFFRACTIONf_angle_d1.1529731
X-RAY DIFFRACTIONf_dihedral_angle_d15.7542448
X-RAY DIFFRACTIONf_chiral_restr0.0711179
X-RAY DIFFRACTIONf_plane_restr0.0041247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61740.56191620.54872832X-RAY DIFFRACTION78
1.6174-1.63640.52261610.4793103X-RAY DIFFRACTION87
1.6364-1.65630.45232000.42073296X-RAY DIFFRACTION92
1.6563-1.67730.3661720.32243428X-RAY DIFFRACTION94
1.6773-1.69940.32781920.25643542X-RAY DIFFRACTION98
1.6994-1.72260.20661750.17823588X-RAY DIFFRACTION99
1.7226-1.74720.20382010.15973566X-RAY DIFFRACTION100
1.7472-1.77330.20322050.15363647X-RAY DIFFRACTION100
1.7733-1.8010.1961940.14423604X-RAY DIFFRACTION100
1.801-1.83050.17131720.13273651X-RAY DIFFRACTION100
1.8305-1.86210.20331860.13873607X-RAY DIFFRACTION100
1.8621-1.8960.18251690.14073663X-RAY DIFFRACTION100
1.896-1.93240.21241740.14753625X-RAY DIFFRACTION100
1.9324-1.97180.21421850.15493632X-RAY DIFFRACTION100
1.9718-2.01470.20711940.16593646X-RAY DIFFRACTION100
2.0147-2.06150.19291960.16623628X-RAY DIFFRACTION100
2.0615-2.11310.17752010.16013629X-RAY DIFFRACTION100
2.1131-2.17020.17791980.15883673X-RAY DIFFRACTION100
2.1702-2.2340.17941810.15123638X-RAY DIFFRACTION100
2.234-2.30610.17321930.15383656X-RAY DIFFRACTION100
2.3061-2.38850.16121860.15293638X-RAY DIFFRACTION100
2.3885-2.4840.19511870.15783661X-RAY DIFFRACTION100
2.484-2.5970.19411930.16633686X-RAY DIFFRACTION100
2.597-2.73380.19642090.17143640X-RAY DIFFRACTION100
2.7338-2.90480.21842010.16353692X-RAY DIFFRACTION100
2.9048-3.12880.19081960.17063690X-RAY DIFFRACTION100
3.1288-3.44310.16522080.15873713X-RAY DIFFRACTION100
3.4431-3.93990.17132090.15523713X-RAY DIFFRACTION100
3.9399-4.95840.15631940.14063767X-RAY DIFFRACTION100
4.9584-26.4250.19281930.18713906X-RAY DIFFRACTION99

+
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://pdbjlvh1.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