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- PDB-6uuv: Crystal structure of a high molecular weight 3-oxoacyl-ACP reduct... -

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Basic information

Entry
Database: PDB / ID: 6uuv
TitleCrystal structure of a high molecular weight 3-oxoacyl-ACP reductase (FabG) from Acinetobacter baumannii crystal form 1
Components3-ketoacyl-ACP reductase
KeywordsOXIDOREDUCTASE / FabG / reductase / HMw / 3-oxoacyl-ACP
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Similarity search - Function
PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
3-oxoacyl-ACP reductase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCross, E.M. / Forwood, J.K.
CitationJournal: Sci Rep / Year: 2021
Title: Insights into Acinetobacter baumannii fatty acid synthesis 3-oxoacyl-ACP reductases.
Authors: Cross, E.M. / Adams, F.G. / Waters, J.K. / Aragao, D. / Eijkelkamp, B.A. / Forwood, J.K.
History
DepositionNov 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 23, 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 1.2Oct 11, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-ketoacyl-ACP reductase
B: 3-ketoacyl-ACP reductase


Theoretical massNumber of molelcules
Total (without water)102,3502
Polymers102,3502
Non-polymers00
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-27 kcal/mol
Surface area30750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.190, 63.650, 64.358
Angle α, β, γ (deg.)69.700, 65.450, 76.630
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein 3-ketoacyl-ACP reductase / 3-oxoacyl-ACP reductase / FabG


Mass: 51175.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: fabG_6, fabG, fabG_28, fabG_3, AB719_16670, CEJ63_16090, EJB02_12225, SAMEA104305229_01073, SAMEA104305325_01586, SAMEA104305337_09390
Production host: Escherichia coli (E. coli)
References: UniProt: A0A219C8F5, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 38.82 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES pH7.5, 10% v/v 2-Propanol, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95366 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95366 Å / Relative weight: 1
ReflectionResolution: 1.8→48.71 Å / Num. obs: 71417 / % possible obs: 96.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.43 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.044 / Rrim(I) all: 0.082 / Net I/σ(I): 9.5
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4191 / CC1/2: 0.809 / Rpim(I) all: 0.273 / Rrim(I) all: 0.487

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Processing

Software
NameVersionClassification
Coot1.13_2998model building
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VP5

5vp5


Resolution: 1.8→48.71 Å / SU ML: 0.2174 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 22.3776
RfactorNum. reflection% reflection
Rfree0.2145 3557 4.98 %
Rwork0.1814 --
obs0.183 71364 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.19 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6406 0 0 271 6677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00686490
X-RAY DIFFRACTIONf_angle_d0.79618816
X-RAY DIFFRACTIONf_chiral_restr0.05661063
X-RAY DIFFRACTIONf_plane_restr0.00511155
X-RAY DIFFRACTIONf_dihedral_angle_d16.73792322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.31011140.26012714X-RAY DIFFRACTION95.64
1.82-1.850.28771790.24912653X-RAY DIFFRACTION95.32
1.85-1.880.27211190.24142687X-RAY DIFFRACTION95.28
1.88-1.910.26551610.23752671X-RAY DIFFRACTION95.35
1.91-1.940.32541510.23182621X-RAY DIFFRACTION95.19
1.94-1.970.26471210.22412747X-RAY DIFFRACTION95.76
1.97-2.010.25061230.21222722X-RAY DIFFRACTION96.08
2.01-2.050.26191390.21042689X-RAY DIFFRACTION95.86
2.05-2.090.29561550.21412675X-RAY DIFFRACTION95.77
2.09-2.130.23881320.20612703X-RAY DIFFRACTION96
2.13-2.180.24181450.20042695X-RAY DIFFRACTION96.3
2.18-2.240.25481310.19522712X-RAY DIFFRACTION96.57
2.24-2.30.25921530.18892717X-RAY DIFFRACTION96.41
2.3-2.370.21631500.19182714X-RAY DIFFRACTION96.79
2.37-2.440.25281490.19032709X-RAY DIFFRACTION96.52
2.44-2.530.25471560.18882697X-RAY DIFFRACTION97.01
2.53-2.630.24921370.19962718X-RAY DIFFRACTION96.94
2.63-2.750.25391410.19682717X-RAY DIFFRACTION97.21
2.75-2.90.21411300.20272766X-RAY DIFFRACTION97.15
2.9-3.080.24891350.19232747X-RAY DIFFRACTION97.43
3.08-3.320.21521390.19342747X-RAY DIFFRACTION97.63
3.32-3.650.19031670.17622711X-RAY DIFFRACTION97.82
3.65-4.180.1641370.14512767X-RAY DIFFRACTION97.91
4.18-5.260.15981400.13192748X-RAY DIFFRACTION97.87
5.26-48.710.14131530.142760X-RAY DIFFRACTION98.48

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