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- PDB-1edo: THE X-RAY STRUCTURE OF BETA-KETO ACYL CARRIER PROTEIN REDUCTASE F... -

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Basic information

Entry
Database: PDB / ID: 1edo
TitleTHE X-RAY STRUCTURE OF BETA-KETO ACYL CARRIER PROTEIN REDUCTASE FROM BRASSICA NAPUS COMPLEXED WITH NADP+
ComponentsBETA-KETO ACYL CARRIER PROTEIN REDUCTASE
KeywordsOXIDOREDUCTASE / nucleotide fold / rossmann fold
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / chloroplast / fatty acid biosynthetic process / NAD binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / short chain dehydrogenase / 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-oxoacyl-(acyl-carrier-protein) reductase / short chain dehydrogenase / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic
Similarity search - Component
Biological speciesBrassica napus (rape)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsFisher, M. / Kroon, J.T. / Martindale, W. / Stuitje, A.R. / Slabas, A.R. / Rafferty, J.B.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: The X-ray structure of Brassica napus beta-keto acyl carrier protein reductase and its implications for substrate binding and catalysis.
Authors: Fisher, M. / Kroon, J.T. / Martindale, W. / Stuitje, A.R. / Slabas, A.R. / Rafferty, J.B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization of the NADP-dependent beta-keto acyl-carrier protein reductase from Brassica napus
Authors: Fisher, M. / Sedelnikova, S.E. / Martindale, W. / Simon, J.W. / Slabas, A.R. / Rafferty, J.B.
History
DepositionJan 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: BETA-KETO ACYL CARRIER PROTEIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1032
Polymers25,3591
Non-polymers7431
Water2,234124
1
A: BETA-KETO ACYL CARRIER PROTEIN REDUCTASE
hetero molecules

A: BETA-KETO ACYL CARRIER PROTEIN REDUCTASE
hetero molecules

A: BETA-KETO ACYL CARRIER PROTEIN REDUCTASE
hetero molecules

A: BETA-KETO ACYL CARRIER PROTEIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4118
Polymers101,4384
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
crystal symmetry operation12_565x,x-y+1,-z+2/31
Buried area17470 Å2
ΔGint-105 kcal/mol
Surface area30410 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)129.280, 129.280, 92.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsThe biological assembly is a tetramer formed from the monomer and generated by 222 symmetry

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Components

#1: Protein BETA-KETO ACYL CARRIER PROTEIN REDUCTASE


Mass: 25359.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica napus (rape) / Gene: OIL SEED RAPE / Production host: Escherichia coli (E. coli) / References: UniProt: Q93X62
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 4.41 Å3/Da / Density % sol: 72.08 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG1500, Sodium citrate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal
*PLUS
Density % sol: 73 %
Crystal grow
*PLUS
Details: Fisher, M., (2000) Acta Crystallogr., Sect.D, 56, 86.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
180 %enzyme1drop
250 mMsodium phosphate1drop
31 mMdithiothreitol1drop
45 mMNADP+1drop
58-12 %(w/v)PEG15001reservoir
6100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 13, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.22→47.9 Å / Num. all: 102604 / Num. obs: 102604 / % possible obs: 95 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.071
Reflection shellResolution: 2.22→2.34 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.45 / Num. unique all: 21256 / % possible all: 91.5
Reflection
*PLUS
Num. obs: 21256 / % possible obs: 95 % / Num. measured all: 102604
Reflection shell
*PLUS
% possible obs: 91.5 % / Rmerge(I) obs: 0.45

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→10 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.235 1041 RANDOM
Rwork0.19 --
all-28417 -
obs-28417 -
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 48 124 1894
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg2.4
X-RAY DIFFRACTIONo_bond_d0.015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 10 Å / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_deg

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