[English] 日本語
Yorodumi
- PDB-4k6f: X-ray crystal structure of a putative Acetoacetyl-CoA reductase f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4k6f
TitleX-ray crystal structure of a putative Acetoacetyl-CoA reductase from Burkholderia cenocepacia bound to the co-factor NADP
ComponentsPutative Acetoacetyl-CoA reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Acetoacetyl-CoA reductase
Function / homology
Function and homology information


acetoacetyl-CoA reductase / acetoacetyl-CoA reductase activity / poly-hydroxybutyrate biosynthetic process / nucleotide binding / cytoplasm
Similarity search - Function
Acetoacetyl-CoA reductase / : / short chain dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...Acetoacetyl-CoA reductase / : / short chain dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Acetoacetyl-CoA reductase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: X-ray crystal structure of a putative Acetoacetyl-CoA reductase from Burkholderia cenocepacia bound to the co-factor NADP
Authors: Fairman, J.W. / Edwards, T.E. / Lorimer, D.
History
DepositionApr 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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: Putative Acetoacetyl-CoA reductase
B: Putative Acetoacetyl-CoA reductase
C: Putative Acetoacetyl-CoA reductase
D: Putative Acetoacetyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0167
Polymers109,7864
Non-polymers2,2303
Water17,024945
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15280 Å2
ΔGint-88 kcal/mol
Surface area33240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.740, 101.330, 134.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Putative Acetoacetyl-CoA reductase


Mass: 27446.385 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: phbB, BceJ2315_08230, BCAL0833 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EAU4, acetoacetyl-CoA reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 945 / 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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: JCSG+ G4: 0.1 M TRIS-HCl, 200 mM trimethylamine N-oxide, 20% PEG 2000 MME , pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.5→47.415 Å / Num. all: 146320 / Num. obs: 145003 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.215 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.78
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.5-1.540.5463.71641151055598.4
1.54-1.580.4474.53627181031798.8
1.58-1.630.3815.25612161003198.8
1.63-1.680.3196.2559752979099.1
1.68-1.730.2757.1357298941698.8
1.73-1.790.2089.0955862920099
1.79-1.860.16711.0553223885499.1
1.86-1.940.13113.2650618857199.3
1.94-2.020.116.6248250825799.3
2.02-2.120.07620.5545258785999.5
2.12-2.240.06124.3143025754299.5
2.24-2.370.05128.3939948711299.6
2.37-2.540.04531.0237307669599.5
2.54-2.740.03935.2434559627299.6
2.74-30.03439.3531552577999.5
3-3.350.02944.6327686525999.5
3.35-3.870.02551.9123914462599.5
3.87-4.740.02456.1620214398099.5
4.74-6.710.02453.8615919312599.3
6.710.02356.18388176497.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K6C

4k6c


Resolution: 1.5→47.46 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.38 / SU B: 3.217 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 7264 5 %RANDOM
Rwork0.1652 ---
obs0.1676 137740 99.13 %-
all-146320 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.9 Å2 / Biso mean: 15.131 Å2 / Biso min: 4.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.38 Å2-0 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.5→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7152 0 118 945 8215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197463
X-RAY DIFFRACTIONr_bond_other_d0.0010.027111
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.96610186
X-RAY DIFFRACTIONr_angle_other_deg0.811316281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6275993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02424.085284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.982151170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2161546
X-RAY DIFFRACTIONr_chiral_restr0.080.21194
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218583
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021660
X-RAY DIFFRACTIONr_mcbond_it1.5721.2123921
X-RAY DIFFRACTIONr_mcbond_other1.5721.2123920
X-RAY DIFFRACTIONr_mcangle_it1.8591.8254898
X-RAY DIFFRACTIONr_rigid_bond_restr2.062314574
X-RAY DIFFRACTIONr_sphericity_free32.6685250
X-RAY DIFFRACTIONr_sphericity_bonded7.913515129
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 512 -
Rwork0.23 10031 -
all-10543 -
obs--98.28 %

+
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