[English] 日本語
Yorodumi
- PDB-6zzo: Crystal structure of (R)-3-hydroxybutyrate dehydrogenase from Psy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zzo
TitleCrystal structure of (R)-3-hydroxybutyrate dehydrogenase from Psychrobacter arcticus complexed with NAD+ and acetoacetate
ComponentsPutative beta-hydroxybutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / (R)-3-hydroxybutyrate dehydrogenase / psychrophilic enzyme / short-chain dehydrogenase/reductase
Function / homology
Function and homology information


3-hydroxybutyrate dehydrogenase / 3-hydroxybutyrate dehydrogenase activity / monocarboxylic acid metabolic process / lipid metabolic process / nucleotide binding
Similarity search - Function
3-hydroxybutyrate dehydrogenase / : / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETOACETIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Putative beta-hydroxybutyrate dehydrogenase
Similarity search - Component
Biological speciesPsychrobacter arcticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsMachado, T.F.G. / da Silva, R.G. / Gloster, T.M. / McMahon, S.A. / Oehler, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: Acs Catalysis / Year: 2020
Title: Dissecting the Mechanism of ( R )-3-Hydroxybutyrate Dehydrogenase by Kinetic Isotope Effects, Protein Crystallography, and Computational Chemistry.
Authors: Machado, T.F.G. / Purg, M. / McMahon, S.A. / Read, B.J. / Oehler, V. / Aqvist, J. / Gloster, T.M. / da Silva, R.G.
History
DepositionAug 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative beta-hydroxybutyrate dehydrogenase
B: Putative beta-hydroxybutyrate dehydrogenase
C: Putative beta-hydroxybutyrate dehydrogenase
D: Putative beta-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,91512
Polymers112,8534
Non-polymers3,0628
Water22,7891265
1
A: Putative beta-hydroxybutyrate dehydrogenase
B: Putative beta-hydroxybutyrate dehydrogenase
hetero molecules

A: Putative beta-hydroxybutyrate dehydrogenase
B: Putative beta-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,91512
Polymers112,8534
Non-polymers3,0628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area21290 Å2
ΔGint-118 kcal/mol
Surface area29740 Å2
MethodPISA
2
C: Putative beta-hydroxybutyrate dehydrogenase
D: Putative beta-hydroxybutyrate dehydrogenase
hetero molecules

C: Putative beta-hydroxybutyrate dehydrogenase
D: Putative beta-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,91512
Polymers112,8534
Non-polymers3,0628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area21170 Å2
ΔGint-114 kcal/mol
Surface area31910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.275, 110.875, 136.903
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-500-

HOH

21C-614-

HOH

31D-678-

HOH

-
Components

#1: Protein
Putative beta-hydroxybutyrate dehydrogenase


Mass: 28213.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter arcticus (bacteria) / Gene: Psyc_1428 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q4FRT2, 3-hydroxybutyrate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-AAE / ACETOACETIC ACID


Mass: 102.089 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1265 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 45% (v/v) MPD, 0.2 M calcium chloride, 0.1 M Bis Tris

-
Data collection

DiffractionMean temperature: 175 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.28→29.51 Å / Num. obs: 266705 / % possible obs: 99.5 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Net I/σ(I): 15.8
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 2 / Num. unique obs: 77229 / CC1/2: 0.77 / Rpim(I) all: 0.343 / % possible all: 92.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q2Q

2q2q


Resolution: 1.28→29.51 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.647 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1608 13358 5 %RANDOM
Rwork0.1424 ---
obs0.1433 253280 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.31 Å2 / Biso mean: 14.224 Å2 / Biso min: 6.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 1.28→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7585 0 232 1311 9128
Biso mean--13.59 28.37 -
Num. residues----1030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138238
X-RAY DIFFRACTIONr_bond_other_d00.0177708
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.6311264
X-RAY DIFFRACTIONr_angle_other_deg1.4381.57417875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47751104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57524.236347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46151335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3451525
X-RAY DIFFRACTIONr_chiral_restr0.0750.21165
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.029394
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021577
LS refinement shellResolution: 1.28→1.311 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.271 977 -
Rwork0.263 17729 -
obs--95.11 %

+
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