[English] 日本語
Yorodumi
- PDB-4o6v: Crystal Structure of a 3-oxoacyl-[acyl-carrier protein] reductase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4o6v
TitleCrystal Structure of a 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) from Brucella suis
ComponentsOxidoreductase, short-chain dehydrogenase/reductase family
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / dehydrogenase
Function / homology: / 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 / Oxidoreductase, short-chain dehydrogenase/reductase family
Function and homology information
Biological speciesBrucella suis ("Organism resembling Bacillus abortus" Traum 1914)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of a 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) from Brucella suis
Authors: Dranow, D.M. / Fairman, J.W. / Edwards, T.E. / Lorimer, D.
History
DepositionDec 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 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: Oxidoreductase, short-chain dehydrogenase/reductase family
B: Oxidoreductase, short-chain dehydrogenase/reductase family
C: Oxidoreductase, short-chain dehydrogenase/reductase family
D: Oxidoreductase, short-chain dehydrogenase/reductase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,27318
Polymers104,0144
Non-polymers1,25914
Water12,683704
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16580 Å2
ΔGint-95 kcal/mol
Surface area29130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.890, 108.360, 115.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Oxidoreductase, short-chain dehydrogenase/reductase family


Mass: 26003.428 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella suis ("Organism resembling Bacillus abortus" Traum 1914)
Strain: ATCC 23445/NCTC 10510 / Gene: BSUIS_A0748 / Production host: Escherichia coli (E. coli)
References: UniProt: B0CL43, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / 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: 2.13 Å3/Da / Density % sol: 42.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MCSG1(b10): 01M MgCl2, 0.08M Tris-HCl, pH=8.5, 24% PEG-400, 20% glyercol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 30, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 76521 / Num. obs: 76352 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 27.826 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.85-1.90.4633.74277495584100
1.9-1.950.384.5826990545199.9
1.95-2.010.2865.926379529899.9
2.01-2.070.2287.4125590515099.9
2.07-2.140.198.7124893501099.9
2.14-2.210.15310.5924134483899.9
2.21-2.290.12612.5923170467799.9
2.29-2.390.10814.29224294508100
2.39-2.490.09316.27214074300100
2.49-2.620.07819.11207194159100
2.62-2.760.06422.41196753956100
2.76-2.930.05326.3318538373099.9
2.93-3.130.04530.4617438351199.7
3.13-3.380.03735.9616406331099.8
3.38-3.70.03141.6414924303099.9
3.7-4.140.02845.8413560276099.8
4.14-4.780.02549.1711943244799.7
4.78-5.850.02647.2810077208499.2
5.85-8.270.02548.767813163998.4
8.270.02351.48387491094

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HQ1

2hq1


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.173 / WRfactor Rwork: 0.1399 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8886 / SU B: 4.803 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1175 / SU Rfree: 0.1107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1807 3839 5 %RANDOM
Rwork0.1458 ---
all0.1476 80191 --
obs0.1476 76352 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.26 Å2 / Biso mean: 24.576 Å2 / Biso min: 6.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å20 Å2
2---0.28 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6832 0 82 704 7618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197063
X-RAY DIFFRACTIONr_bond_other_d0.0010.026715
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.969570
X-RAY DIFFRACTIONr_angle_other_deg0.83315372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2445931
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9323.943279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.657151089
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3471549
X-RAY DIFFRACTIONr_chiral_restr0.0910.21109
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218129
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021578
X-RAY DIFFRACTIONr_mcbond_it1.0361.3913721
X-RAY DIFFRACTIONr_mcbond_other1.0361.3913720
X-RAY DIFFRACTIONr_mcangle_it1.6162.0784647
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 285 -
Rwork0.186 5285 -
all-5570 -
obs--99.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.28680.14290.97780.8735-0.09311.4971-0.0163-0.0225-0.2144-0.10550.01430.00070.0182-0.04870.00190.04370.021600.1003-0.030.077524.838113.2221-1.5695
21.0114-0.2099-0.41570.5460.24050.67910.02010.1174-0.0699-0.0084-0.0357-0.00120.0766-0.06010.01560.02960.0094-0.00960.0641-0.00640.082916.562412.37759.8369
30.6129-0.2781-0.09081.002-0.08440.43090.02790.0448-0.0147-0.04-0.02190.05260.02450.0009-0.0060.01920.0103-0.01160.0761-0.0090.085721.344525.289512.4372
42.20480.0543-0.14041.5657-0.32521.6310.1297-0.23650.13270.0847-0.048-0.0905-0.13020.2127-0.08180.0302-0.06240.01840.1506-0.04520.083545.426842.795518.8927
50.59390.2743-0.66540.616-0.08161.21930.0358-0.13360.04820.0523-0.0276-0.1173-0.04820.1955-0.00820.0272-0.011-0.02170.1053-0.01590.109731.487939.831929.7197
60.4557-0.0972-0.18090.7114-0.19280.4748-0.0012-0.04940.05080.05850.0104-0.0714-0.02510.0831-0.00920.02180.0004-0.00980.0848-0.01410.08831.140628.813222.352
71.74290.0744-0.28841.5678-0.21233.0434-0.0711-0.34160.24770.22250.00680.1722-0.3933-0.07260.06430.25370.01280.06480.1106-0.07660.0924.420844.10752.9434
80.7330.1477-0.76590.6503-0.21741.46540.0828-0.13860.12070.2088-0.0043-0.0199-0.13450.0428-0.07850.0963-0.01430.0060.0753-0.03610.064616.38842.038242.9122
90.9268-0.14820.09570.7091-0.12170.8152-0.0123-0.05850.08530.1561-0.00270.1105-0.0735-0.01910.0150.0490.00250.02710.0495-0.01560.07855.543235.402136.1331
102.06340.44330.92161.789-0.18910.85230.0637-0.0329-0.15010.1149-0.09610.10890.1195-0.12750.03230.0546-0.04110.08030.0884-0.02870.1901-12.32512.998533.9567
111.1961-0.0383-0.31640.51960.45910.5491-0.0472-0.067-0.10480.0928-0.00940.06570.1276-0.03220.05660.0553-0.01470.02080.05310.01670.11483.837612.770124.4872
120.9298-0.18790.09180.45480.01720.90130.0015-0.0493-0.06830.1102-0.02480.1150.1169-0.01250.02320.0524-0.01060.02850.04790.00420.10385.387620.865635.6899
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 60
2X-RAY DIFFRACTION2A61 - 150
3X-RAY DIFFRACTION3A151 - 234
4X-RAY DIFFRACTION4B3 - 73
5X-RAY DIFFRACTION5B74 - 154
6X-RAY DIFFRACTION6B155 - 234
7X-RAY DIFFRACTION7C0 - 60
8X-RAY DIFFRACTION8C61 - 159
9X-RAY DIFFRACTION9C160 - 234
10X-RAY DIFFRACTION10D3 - 84
11X-RAY DIFFRACTION11D85 - 153
12X-RAY DIFFRACTION12D154 - 234

+
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