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- PDB-6wpr: Crystal structure of a putative 3-oxoacyl-ACP reductase (FabG) wi... -

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Basic information

Entry
Database: PDB / ID: 6wpr
TitleCrystal structure of a putative 3-oxoacyl-ACP reductase (FabG) with NADP(H) from Acinetobacter baumannii
Components3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE / FabG / reductase / SDR / Rossmann Fold
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid biosynthetic process / NAD binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
DepositionApr 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: 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 18, 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-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7444
Polymers52,2532
Non-polymers1,4912
Water8,917495
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
hetero molecules

A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4888
Polymers104,5074
Non-polymers2,9824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area17140 Å2
ΔGint-85 kcal/mol
Surface area33840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.430, 87.430, 151.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-602-

HOH

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] reductase


Mass: 26126.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: fabG_9, fabG, fabG_5, fabG_8, A7M79_02495, A7M90_13795, A9843_07395, AA954_11685, ABCAM1_0760, ABUW_3108, APD33_00335, B4R90_07750, B9W69_04055, B9X95_05710, BGC29_09155, C2U32_18365, CEJ64_ ...Gene: fabG_9, fabG, fabG_5, fabG_8, A7M79_02495, A7M90_13795, A9843_07395, AA954_11685, ABCAM1_0760, ABUW_3108, APD33_00335, B4R90_07750, B9W69_04055, B9X95_05710, BGC29_09155, C2U32_18365, CEJ64_13010, CHQ89_11440, CPI82_11015, CSB70_0489, DLI69_06485, DLI75_02490, DOL94_00645, DVA79_16530, E2533_13485, E2536_16310, E5294_15795, E5979_01830, EA685_06995, EA746_003475, EKS29_20225, EWO92_12305, EWO96_16390, EWP49_14850, FD887_09475, FD913_04775, FJU36_15155, FJU42_04975, FJU76_14990, FJU79_09000, FJU87_10860, FJV14_09530, LV38_02926, NCTC13305_01645, NCTC13420_02176, NT90_07375, SAMEA104305318_02347, SAMEA104305351_01934
Production host: Escherichia coli (E. coli)
References: UniProt: V5VHN7, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, pH 8.0, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 28, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.85→50.55 Å / Num. obs: 51013 / % possible obs: 100 % / Redundancy: 14.3 % / Biso Wilson estimate: 18.94 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.021 / Rrim(I) all: 0.08 / Net I/σ(I): 26.3
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 3085 / CC1/2: 0.939 / Rpim(I) all: 0.158 / Rrim(I) all: 0.606

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Processing

Software
NameVersionClassification
REFMAC1.18.2_3874refinement
PHENIX1.18.2_3874refinement
MOSFLM1.17.1_3660data reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6UDS

6uds


Resolution: 1.85→47.91 Å / SU ML: 0.1834 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.9494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1905 2556 5.02 %
Rwork0.1605 48374 -
obs0.162 50930 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.53 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3595 0 96 495 4186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01053748
X-RAY DIFFRACTIONf_angle_d1.07335082
X-RAY DIFFRACTIONf_chiral_restr0.0575591
X-RAY DIFFRACTIONf_plane_restr0.0062653
X-RAY DIFFRACTIONf_dihedral_angle_d18.70611350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.28521370.21432630X-RAY DIFFRACTION100
1.89-1.920.24551430.19192654X-RAY DIFFRACTION100
1.92-1.970.23921580.182613X-RAY DIFFRACTION100
1.97-2.010.19681380.16982649X-RAY DIFFRACTION100
2.01-2.060.24811430.17012660X-RAY DIFFRACTION100
2.06-2.120.19751380.16252629X-RAY DIFFRACTION100
2.12-2.180.19311480.15862655X-RAY DIFFRACTION100
2.18-2.250.18211390.15612665X-RAY DIFFRACTION100
2.25-2.330.17921320.14382668X-RAY DIFFRACTION99.96
2.33-2.420.17651570.1422643X-RAY DIFFRACTION100
2.42-2.530.16661360.14982672X-RAY DIFFRACTION100
2.53-2.670.18721220.15892683X-RAY DIFFRACTION100
2.67-2.840.19751380.16522702X-RAY DIFFRACTION100
2.84-3.050.18481590.17072683X-RAY DIFFRACTION100
3.05-3.360.19581310.16652727X-RAY DIFFRACTION100
3.36-3.850.16671290.14922745X-RAY DIFFRACTION100
3.85-4.850.1511490.13072765X-RAY DIFFRACTION100
4.85-47.910.21791590.18762931X-RAY DIFFRACTION99.87

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