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- PDB-4nbv: Crystal structure of FabG from Cupriavidus taiwanensis -

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Basic information

Entry
Database: PDB / ID: 4nbv
TitleCrystal structure of FabG from Cupriavidus taiwanensis
Components3-oxoacyl-[acyl-carrier-protein] reductase putative short-chain dehydrogenases/reductases (SDR) family protein
KeywordsOXIDOREDUCTASE / reductase
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase
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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-oxoacyl-[acyl-carrier-protein] reductase putative short-chain dehydrogenases/reductases (SDR) family protein
Similarity search - Component
Biological speciesCupriavidus taiwanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.645 Å
AuthorsPereira, J.H. / Mcandrew, R.P. / Javidpour, P. / Beller, H.R. / Adams, P.D.
CitationJournal: Appl.Environ.Microbiol. / Year: 2014
Title: Biochemical and Structural Studies of NADH-Dependent FabG Used To Increase the Bacterial Production of Fatty Acids under Anaerobic Conditions.
Authors: Javidpour, P. / Pereira, J.H. / Goh, E.B. / McAndrew, R.P. / Ma, S.M. / Friedland, G.D. / Keasling, J.D. / Chhabra, S.R. / Adams, P.D. / Beller, H.R.
History
DepositionOct 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 putative short-chain dehydrogenases/reductases (SDR) family protein
B: 3-oxoacyl-[acyl-carrier-protein] reductase putative short-chain dehydrogenases/reductases (SDR) family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8253
Polymers51,5432
Non-polymers2821
Water9,224512
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase putative short-chain dehydrogenases/reductases (SDR) family protein
B: 3-oxoacyl-[acyl-carrier-protein] reductase putative short-chain dehydrogenases/reductases (SDR) family protein
hetero molecules

A: 3-oxoacyl-[acyl-carrier-protein] reductase putative short-chain dehydrogenases/reductases (SDR) family protein
B: 3-oxoacyl-[acyl-carrier-protein] reductase putative short-chain dehydrogenases/reductases (SDR) family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6516
Polymers103,0864
Non-polymers5652
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area12110 Å2
ΔGint-68 kcal/mol
Surface area32690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.763, 111.763, 79.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-554-

HOH

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] reductase putative short-chain dehydrogenases/reductases (SDR) family protein


Mass: 25771.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus taiwanensis (bacteria) / Strain: R1 / LMG 19424 / Gene: RALTA_A2639 / Production host: Escherichia coli (E. coli)
References: UniProt: B3R6T4, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.1 Sodium Malonate pH 7.0, 0.03 M Citric Acid, 0.07 M Bis-Tris propane pH 7.6 and 20 % PEG 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2012
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→37.325 Å / Num. all: 58825 / Num. obs: 58825 / % possible obs: 95.95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.645→1.6857 Å / % possible all: 95.95

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Processing

Software
NameVersionClassification
BOSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q7B

1q7b


Resolution: 1.645→35.403 Å / SU ML: 0.12 / σ(F): 0 / Phase error: 14.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1543 1946 3.31 %
Rwork0.1362 --
obs0.1368 58824 95.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.645→35.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3612 0 19 512 4143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093674
X-RAY DIFFRACTIONf_angle_d1.1734981
X-RAY DIFFRACTIONf_dihedral_angle_d12.5991318
X-RAY DIFFRACTIONf_chiral_restr0.05592
X-RAY DIFFRACTIONf_plane_restr0.005648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6445-1.68570.29011060.22883227X-RAY DIFFRACTION77
1.6857-1.73120.19171340.17843765X-RAY DIFFRACTION90
1.7312-1.78220.17591340.15583915X-RAY DIFFRACTION94
1.7822-1.83970.16821390.13943940X-RAY DIFFRACTION94
1.8397-1.90550.16181330.13754009X-RAY DIFFRACTION96
1.9055-1.98170.15791400.12894058X-RAY DIFFRACTION97
1.9817-2.07190.14191420.12864115X-RAY DIFFRACTION98
2.0719-2.18110.15841430.12524147X-RAY DIFFRACTION99
2.1811-2.31780.15551430.12614163X-RAY DIFFRACTION99
2.3178-2.49670.14671410.12324198X-RAY DIFFRACTION99
2.4967-2.74790.15411450.13594229X-RAY DIFFRACTION100
2.7479-3.14530.14641450.13154266X-RAY DIFFRACTION100
3.1453-3.96190.14351470.13614329X-RAY DIFFRACTION100
3.9619-35.41140.15251540.13834517X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 37.3849 Å / Origin y: 39.9217 Å / Origin z: 24.1435 Å
111213212223313233
T0.1404 Å2-0.0078 Å20.008 Å2-0.1361 Å20.0054 Å2--0.1348 Å2
L0.3573 °2-0.1517 °20.0904 °2-0.3206 °2-0.1236 °2--0.4433 °2
S0.014 Å °0.093 Å °0.0365 Å °-0.0445 Å °-0.0322 Å °-0.0253 Å °-0.0257 Å °0.0474 Å °-0.0424 Å °
Refinement TLS groupSelection details: all

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