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- PDB-7czc: Crystal structure of apo-FabG from Vibrio harveyi -

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Basic information

Entry
Database: PDB / ID: 7czc
TitleCrystal structure of apo-FabG from Vibrio harveyi
Components3-oxoacyl-ACP reductase FabG
KeywordsOXIDOREDUCTASE / 3-oxo-acyl-ACP reductase / Rossmann fold / SDR-family / fatty acid metabolism
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / oxidoreductase activity
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase, putative / : / PKS_KR / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 3-oxoacyl-ACP reductase FabG
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSingh, B.K. / Kumar, A. / Paul, B. / Biswas, R. / Das, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR12404/BRB/10/1362/2014 India
CitationJournal: To Be Published
Title: Crystal structure of apo-FabG from Vibrio harveyi
Authors: Singh, B.K. / Kumar, A. / Paul, B. / Biswas, R. / Das, A.K.
History
DepositionSep 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-ACP reductase FabG
B: 3-oxoacyl-ACP reductase FabG
C: 3-oxoacyl-ACP reductase FabG
D: 3-oxoacyl-ACP reductase FabG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1276
Polymers103,9154
Non-polymers2122
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12320 Å2
ΔGint-69 kcal/mol
Surface area34910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.459, 91.320, 94.158
Angle α, β, γ (deg.)90.000, 103.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-oxoacyl-ACP reductase FabG / Short chain dehydrogenase family protein


Mass: 25978.738 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: AL538_14035, VCHENC02_3091 / Production host: Escherichia coli M15 (bacteria) / References: UniProt: K5VE97
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.15M DL-malic acid (pH 7.2) , 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→19.7504 Å / Num. obs: 65055 / % possible obs: 99.83 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 21.02
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 6451 / CC1/2: 0.858

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I01

1i01


Resolution: 2→19.749 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 3161 4.93 %
Rwork0.2094 60945 -
obs0.2106 64106 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.66 Å2 / Biso mean: 31.6565 Å2 / Biso min: 15.45 Å2
Refinement stepCycle: final / Resolution: 2→19.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7090 0 34 384 7508
Biso mean--35.93 26.69 -
Num. residues----951
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02930.26461550.2394264299
2.0293-2.0610.24881440.22942660100
2.061-2.09470.28461360.22622708100
2.0947-2.13080.25351240.21852660100
2.1308-2.16950.27971250.22612732100
2.1695-2.21120.35611260.3038255097
2.2112-2.25630.53681220.5066233786
2.2563-2.30530.44611170.4011228586
2.3053-2.35880.28521390.21712697100
2.3588-2.41770.25051320.20182660100
2.4177-2.48290.25731240.20842692100
2.4829-2.55590.22211460.21172687100
2.5559-2.63820.25071380.20662687100
2.6382-2.73220.22991410.20462661100
2.7322-2.84130.20731440.20692680100
2.8413-2.97020.24861410.20312704100
2.9702-3.12620.23541350.21022695100
3.1262-3.32120.23531610.19792653100
3.3212-3.57630.18981500.18932685100
3.5763-3.93360.22931440.191269499
3.9336-4.4970.16371290.15512726100
4.497-5.64370.18191500.15372682100
5.6437-19.7490.15221380.17272768100

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