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- PDB-4dry: The crystal structure of 3-oxoacyl-[acyl-carrier-protein] reducta... -

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Basic information

Entry
Database: PDB / ID: 4dry
TitleThe crystal structure of 3-oxoacyl-[acyl-carrier-protein] reductase from Rhizobium 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 (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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: 2.5 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 from Rhizobium meliloti
Authors: Zhang, Z. / Almo, S.C. / Swaminathan, S.
History
DepositionFeb 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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
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)119,6208
Polymers119,2364
Non-polymers3844
Water3,981221
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15840 Å2
ΔGint-157 kcal/mol
Surface area33250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.531, 98.128, 117.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 29808.947 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: RB1369, SM_b20662 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q92TX5, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M Ammonium Sulfate, 0.1 M MES monohydrate pH 6.5 10% v/v 1,4-Dixane, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9787 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 35258 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Rmerge(I) obs: 0.185 / Net I/σ(I): 15.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 8.6 / Num. unique all: 3489 / % 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: 2.5→49.064 Å / SU ML: 0.37 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.08 / Phase error: 24.83 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2637 1742 5.01 %RANDOM
Rwork0.2062 ---
obs0.2091 34751 98.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.048 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6894 Å20 Å2-0 Å2
2--2.4858 Å20 Å2
3----3.1752 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7115 0 20 221 7356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077234
X-RAY DIFFRACTIONf_angle_d1.059855
X-RAY DIFFRACTIONf_dihedral_angle_d16.2982585
X-RAY DIFFRACTIONf_chiral_restr0.0641184
X-RAY DIFFRACTIONf_plane_restr0.0051306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.57380.25871260.1932695X-RAY DIFFRACTION97
2.5738-2.65690.25711270.20222680X-RAY DIFFRACTION97
2.6569-2.75180.29871500.21912666X-RAY DIFFRACTION98
2.7518-2.8620.28021520.22142698X-RAY DIFFRACTION98
2.862-2.99220.25471600.21992690X-RAY DIFFRACTION98
2.9922-3.150.28861330.22142719X-RAY DIFFRACTION98
3.15-3.34730.28141400.22312757X-RAY DIFFRACTION99
3.3473-3.60560.30071510.20552752X-RAY DIFFRACTION99
3.6056-3.96830.25381580.19032759X-RAY DIFFRACTION100
3.9683-4.54220.2151390.16522813X-RAY DIFFRACTION100
4.5422-5.72130.2261530.18192823X-RAY DIFFRACTION100
5.7213-49.07340.25641530.22082957X-RAY DIFFRACTION99

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