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- PDB-3f9i: Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase ... -

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Basic information

Entry
Database: PDB / ID: 3f9i
TitleCrystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase Rickettsia prowazekii
Components3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE / 3-ketoacyl-(acyl-carrier-protein) reductase / Rickettsia / Fatty acid biosynthesis / Lipid synthesis / NADP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


: / : / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / NAD binding / NADP binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / 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 FabG
Similarity search - Component
Biological speciesRickettsia prowazekii (bacteria)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of 3-ketoacyl-(acyl-carrier-protein) reductase from Rickettsia prowazekii at 2.25 A resolution.
Authors: Subramanian, S. / Abendroth, J. / Phan, I.Q. / Olsen, C. / Staker, B.L. / Napuli, A. / Van Voorhis, W.C. / Stacy, R. / Myler, P.J.
History
DepositionNov 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Sep 6, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)53,6382
Polymers53,6382
Non-polymers00
Water2,324129
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase

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


Theoretical massNumber of molelcules
Total (without water)107,2764
Polymers107,2764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10270 Å2
ΔGint-97 kcal/mol
Surface area32510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.160, 74.160, 183.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 5 / Auth seq-ID: 1 - 241 / Label seq-ID: 9 - 249

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 26818.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia prowazekii (bacteria) / Gene: fabG, RP762 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P50941, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: JCSG+ SCREEN D3: 100MM NA/K PO4, 50% PEG 200, 200MM NACL, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→19.61 Å / Num. obs: 24573 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.7
Reflection shellResolution: 2.25→2.31 Å / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.3 / % possible all: 93

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0063refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: molecular replacement
Starting model: pdb entry 3emk modified by ccp4 program chainsaw

3emk


Resolution: 2.25→19.61 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / SU B: 7.351 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1256 5.1 %RANDOM
Rwork0.213 ---
all0.216 24573 --
obs0.216 24573 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.25→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 0 129 3381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223279
X-RAY DIFFRACTIONr_bond_other_d0.0030.022121
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9734427
X-RAY DIFFRACTIONr_angle_other_deg0.93935249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6925442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18225.714112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26415572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.211511
X-RAY DIFFRACTIONr_chiral_restr0.0850.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023649
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02582
X-RAY DIFFRACTIONr_mcbond_it0.8531.52204
X-RAY DIFFRACTIONr_mcbond_other0.2341.5930
X-RAY DIFFRACTIONr_mcangle_it1.57123502
X-RAY DIFFRACTIONr_scbond_it2.12331075
X-RAY DIFFRACTIONr_scangle_it3.4694.5925
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1294medium positional0.250.5
A1285loose positional0.545
B1294medium thermal1.62
B1285loose thermal1.4210
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 79 -
Rwork0.297 1588 -
obs--92.92 %

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