[English] 日本語
Yorodumi
- PDB-4pze: Crystal structure of (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pze
TitleCrystal structure of (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 in complex with acetoacetyl-CoA
Components3-Hydroxyacyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann Fold
Function / homology
Function and homology information


3-hydroxyacyl-CoA dehydrogenase / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / catabolic process / NAD+ binding / fatty acid metabolic process
Similarity search - Function
3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 ...3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETOACETYL-COENZYME A / 3-Hydroxyacyl-CoA dehydrogenase
Similarity search - Component
Biological speciesRalstonia eutropha H16 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsKim, J. / Chang, J.H. / Kim, K.J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystal structure and biochemical properties of the (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 from Ralstonia eutropha
Authors: Kim, J. / Chang, J.H. / Kim, K.J.
History
DepositionMar 29, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Derived calculations
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 3-Hydroxyacyl-CoA dehydrogenase
B: 3-Hydroxyacyl-CoA dehydrogenase
C: 3-Hydroxyacyl-CoA dehydrogenase
D: 3-Hydroxyacyl-CoA dehydrogenase
E: 3-Hydroxyacyl-CoA dehydrogenase
F: 3-Hydroxyacyl-CoA dehydrogenase
G: 3-Hydroxyacyl-CoA dehydrogenase
H: 3-Hydroxyacyl-CoA dehydrogenase
I: 3-Hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,99818
Polymers272,3349
Non-polymers7,6649
Water2,036113
1
A: 3-Hydroxyacyl-CoA dehydrogenase
hetero molecules

A: 3-Hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2224
Polymers60,5192
Non-polymers1,7032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area5520 Å2
ΔGint-22 kcal/mol
Surface area24630 Å2
MethodPISA
2
B: 3-Hydroxyacyl-CoA dehydrogenase
C: 3-Hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2224
Polymers60,5192
Non-polymers1,7032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-28 kcal/mol
Surface area24400 Å2
MethodPISA
3
D: 3-Hydroxyacyl-CoA dehydrogenase
G: 3-Hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2224
Polymers60,5192
Non-polymers1,7032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-23 kcal/mol
Surface area24420 Å2
MethodPISA
4
E: 3-Hydroxyacyl-CoA dehydrogenase
F: 3-Hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2224
Polymers60,5192
Non-polymers1,7032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-20 kcal/mol
Surface area23390 Å2
MethodPISA
5
H: 3-Hydroxyacyl-CoA dehydrogenase
I: 3-Hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2224
Polymers60,5192
Non-polymers1,7032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-23 kcal/mol
Surface area25130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.243, 135.373, 97.356
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
3-Hydroxyacyl-CoA dehydrogenase


Mass: 30259.309 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha H16 (bacteria) / Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: paaH1, H16_A0282 / Production host: Escherichia coli (E. coli)
References: UniProt: Q0KEY8, 3-hydroxyacyl-CoA dehydrogenase
#2: Chemical
ChemComp-CAA / ACETOACETYL-COENZYME A


Mass: 851.607 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 295 K / pH: 6.5
Details: 2M (NH4)2SO4, 0.1M Cacodylate pH 6.5 and 0.2M Sodium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 16, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 76529
Reflection shellResolution: 2.7→2.8 Å / % possible all: 94

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.885 / SU B: 15.733 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R Free: 0.421 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.285 3770 5 %RANDOM
Rwork0.21 ---
obs0.213 71952 90.7 %-
all-79295 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.05 Å2
Baniso -1Baniso -2Baniso -3
1-3.62 Å20 Å20.5 Å2
2--4.53 Å2-0 Å2
3----8.15 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18918 0 486 113 19517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01919656
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219629
X-RAY DIFFRACTIONr_angle_refined_deg1.5842.01526658
X-RAY DIFFRACTIONr_angle_other_deg0.856345198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74952538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.71924.658657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.699153465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2581599
X-RAY DIFFRACTIONr_chiral_restr0.0850.23222
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221672
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023870
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_it4.5136.91110179
X-RAY DIFFRACTIONr_mcbond_other4.5136.91110178
X-RAY DIFFRACTIONr_mcangle_it6.76710.35212708
X-RAY DIFFRACTIONr_mcangle_other6.76710.35312709
X-RAY DIFFRACTIONr_scbond_it4.9287.6869477
X-RAY DIFFRACTIONr_scbond_other4.9277.6879478
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.51211.40213951
X-RAY DIFFRACTIONr_long_range_B_refined10.34756.54922142
X-RAY DIFFRACTIONr_long_range_B_other10.34756.55322143
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 245 -
Rwork0.318 5182 -
obs--88.62 %

+
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