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- PDB-3u9l: The crystal structure of 3-oxoacyl-[acyl-carrier-protein] reducta... -

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Basic information

Entry
Database: PDB / ID: 3u9l
TitleThe crystal structure of 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) from Sinorhizobium meliloti
Components3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
Similarity search - Function
: / short chain dehydrogenase / PKS_KR / 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
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsZhang, Z. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Zhang, Z. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: TO BE PUBLISHED
Title: The crystal structure of 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) from Sinorhizobium meliloti
Authors: Zhang, Z. / Almo, S.C. / Swaminathan, S.
History
DepositionOct 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)35,4771
Polymers35,4771
Non-polymers00
Water3,531196
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase

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


Theoretical massNumber of molelcules
Total (without water)70,9542
Polymers70,9542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+11
Buried area6020 Å2
ΔGint-30 kcal/mol
Surface area21320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.632, 106.123, 128.796
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-398-

HOH

21A-446-

HOH

31A-469-

HOH

41A-502-

HOH

51A-510-

HOH

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Components

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


Mass: 35476.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: RB0474, SM_b20492 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q92W71, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Potassum sodium tartrate tetrahydrate, 0.1 M sodium citrate tribasic dihydrate pH 5.6, 2.0 M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 23275 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 8.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 8.8 / Num. unique all: 5684 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→40.951 Å / SU ML: 0.28 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.05 / Phase error: 22.32 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 1179 5.07 %RANDOM
Rwork0.1842 ---
obs0.1869 23275 97.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.773 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.7212 Å20 Å2-0 Å2
2--10.5879 Å20 Å2
3----0.8667 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 0 0 196 2355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.022199
X-RAY DIFFRACTIONf_angle_d1.6842980
X-RAY DIFFRACTIONf_dihedral_angle_d16.422796
X-RAY DIFFRACTIONf_chiral_restr0.108336
X-RAY DIFFRACTIONf_plane_restr0.008396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.19560.25841290.18632658X-RAY DIFFRACTION95
2.1956-2.31130.26391410.18272626X-RAY DIFFRACTION95
2.3113-2.45610.25271410.18332719X-RAY DIFFRACTION96
2.4561-2.64570.25281620.19072689X-RAY DIFFRACTION97
2.6457-2.91190.22351340.1842778X-RAY DIFFRACTION98
2.9119-3.33310.2391440.18652803X-RAY DIFFRACTION99
3.3331-4.19870.2151710.16722856X-RAY DIFFRACTION100
4.1987-40.95890.23181570.19332967X-RAY DIFFRACTION100

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