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- PDB-7krm: Putative FabG bound to NADH from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 7krm
TitlePutative FabG bound to NADH from Acinetobacter baumannii
Components3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE / FabG / Acinetobacter baumannii / enzyme
Function / homology
Function and homology information


glucose 1-dehydrogenase [NAD(P)+] activity / glucose 1-dehydrogenase [NAD(P)+] / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / nucleotide binding
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShaw, K.I. / Smith, K.M. / Cross, E.M.
CitationJournal: To Be Published
Title: Putative FabG bound to NADH from Acinetobacter baumannii
Authors: Forwood, J.K.
History
DepositionNov 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
C: 3-oxoacyl-[acyl-carrier-protein] reductase
D: 3-oxoacyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1008
Polymers103,4464
Non-polymers2,6544
Water14,394799
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17560 Å2
ΔGint-73 kcal/mol
Surface area30900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.872, 189.872, 71.981
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein
3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase FabG / Glucose 1-dehydrogenase / SDR family oxidoreductase


Mass: 25861.596 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: fabG_1, ABC003_00909, ABUW_2930, DLI69_07500, EA686_12865, FDO31_05475, GNY86_08660
Production host: Escherichia coli (E. coli)
References: UniProt: A0A077GFB1, glucose 1-dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 799 / 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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate trihydrate, pH 4.6, 2 M sodium formate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→29.91 Å / Num. obs: 76202 / % possible obs: 99.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 16.87 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.2
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 4540 / CC1/2: 0.918

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7KRK

7krk


Resolution: 1.9→29.91 Å / SU ML: 0.1533 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 16.3282 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1739 3837 5.04 %
Rwork0.1505 72334 -
obs0.1516 76171 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6917 0 176 799 7892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00227187
X-RAY DIFFRACTIONf_angle_d0.43499736
X-RAY DIFFRACTIONf_chiral_restr0.04121155
X-RAY DIFFRACTIONf_plane_restr0.00291256
X-RAY DIFFRACTIONf_dihedral_angle_d10.99034242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.20891260.17282656X-RAY DIFFRACTION99.96
1.92-1.950.23371640.17712659X-RAY DIFFRACTION100
1.95-1.980.20961560.1692638X-RAY DIFFRACTION99.93
1.98-20.18941140.15682776X-RAY DIFFRACTION100
2-2.030.18531640.15022633X-RAY DIFFRACTION99.93
2.03-2.070.18991340.15972715X-RAY DIFFRACTION100
2.07-2.10.20761280.16282651X-RAY DIFFRACTION100
2.1-2.140.18571290.15412720X-RAY DIFFRACTION99.96
2.14-2.170.1921470.15312676X-RAY DIFFRACTION100
2.17-2.220.19141630.1472641X-RAY DIFFRACTION100
2.22-2.260.19221680.15112662X-RAY DIFFRACTION99.82
2.26-2.310.19171390.14862692X-RAY DIFFRACTION100
2.31-2.360.15931410.14452653X-RAY DIFFRACTION99.96
2.36-2.420.18431370.14362706X-RAY DIFFRACTION99.96
2.42-2.490.15721510.14362686X-RAY DIFFRACTION99.96
2.49-2.560.17781320.14472667X-RAY DIFFRACTION99.82
2.56-2.650.18241640.14682650X-RAY DIFFRACTION99.96
2.65-2.740.16911500.15312675X-RAY DIFFRACTION99.96
2.74-2.850.18921570.15172685X-RAY DIFFRACTION99.96
2.85-2.980.19471170.15662687X-RAY DIFFRACTION100
2.98-3.140.17311180.15882716X-RAY DIFFRACTION100
3.14-3.330.15831450.15892675X-RAY DIFFRACTION100
3.33-3.590.1631360.1412671X-RAY DIFFRACTION99.96
3.59-3.950.13511620.13292666X-RAY DIFFRACTION100
3.95-4.520.1351100.13052732X-RAY DIFFRACTION99.89
4.52-5.690.16541450.14212664X-RAY DIFFRACTION99.93
5.69-29.910.18271400.17922682X-RAY DIFFRACTION99.82

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