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- PDB-1i01: CRYSTAL STRUCTURE OF BETA-KETOACYL [ACYL CARRIER PROTEIN] REDUCTA... -

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Basic information

Entry
Database: PDB / ID: 1i01
TitleCRYSTAL STRUCTURE OF BETA-KETOACYL [ACYL CARRIER PROTEIN] REDUCTASE FROM E. COLI.
ComponentsBETA-KETOACYL [ACP] REDUCTASE
KeywordsOXIDOREDUCTASE / rossmann fold
Function / homology
Function and homology information


biotin biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / lipid biosynthetic process / NAD binding / fatty acid biosynthetic process / NADP binding / metal ion binding ...biotin biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / lipid biosynthetic process / NAD binding / fatty acid biosynthetic process / NADP binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / : / 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 / : / 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 FabG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsPrice, A.C. / Rock, C.O. / White, S.W.
CitationJournal: Biochemistry / Year: 2001
Title: Structure of beta-ketoacyl-[acyl carrier protein] reductase from Escherichia coli: negative cooperativity and its structural basis.
Authors: Price, A.C. / Zhang, Y.M. / Rock, C.O. / White, S.W.
History
DepositionJan 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 600HETEROGEN HOH 1-36 IS ASSOCIATED WITH CHAIN A. HOH 101-136 IS ASSOCIATED WITH CHAIN B. HOH 201-236 ...HETEROGEN HOH 1-36 IS ASSOCIATED WITH CHAIN A. HOH 101-136 IS ASSOCIATED WITH CHAIN B. HOH 201-236 IS ASSOCIATED WITH CHAIN C. HOH 301-336 IS ASSOCIATED WITH CHAIN D. HOH 401-436 IS ASSOCIATED WITH CHAIN E. HOH 501-536 IS ASSOCIATED WITH CHAIN F. HOH 601-636 IS ASSOCIATED WITH CHAIN G. HOH 701-736 IS ASSOCIATED WITH CHAIN H.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-KETOACYL [ACP] REDUCTASE
B: BETA-KETOACYL [ACP] REDUCTASE
C: BETA-KETOACYL [ACP] REDUCTASE
D: BETA-KETOACYL [ACP] REDUCTASE
E: BETA-KETOACYL [ACP] REDUCTASE
F: BETA-KETOACYL [ACP] REDUCTASE
G: BETA-KETOACYL [ACP] REDUCTASE
H: BETA-KETOACYL [ACP] REDUCTASE


Theoretical massNumber of molelcules
Total (without water)204,6988
Polymers204,6988
Non-polymers00
Water6,287349
1
A: BETA-KETOACYL [ACP] REDUCTASE
B: BETA-KETOACYL [ACP] REDUCTASE
C: BETA-KETOACYL [ACP] REDUCTASE
D: BETA-KETOACYL [ACP] REDUCTASE


Theoretical massNumber of molelcules
Total (without water)102,3494
Polymers102,3494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9990 Å2
ΔGint-61 kcal/mol
Surface area35940 Å2
MethodPISA
2
E: BETA-KETOACYL [ACP] REDUCTASE
F: BETA-KETOACYL [ACP] REDUCTASE
G: BETA-KETOACYL [ACP] REDUCTASE
H: BETA-KETOACYL [ACP] REDUCTASE


Theoretical massNumber of molelcules
Total (without water)102,3494
Polymers102,3494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-64 kcal/mol
Surface area35560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.7, 120.1, 131.1
Angle α, β, γ (deg.)90.0, 90.5, 90.0
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a tetramer formed by molecules A, B, C, and D. / The biological assembly is a tetramer formed by molecules E, F, G, and H.

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Components

#1: Protein
BETA-KETOACYL [ACP] REDUCTASE / 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE / 3-KETOACYL-ACYL CARRIER PROTEIN REDUCTASE


Mass: 25587.277 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEK2, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 10000, Hepes, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 7.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMTris-HCl1droppH7.9
21 mMdithiothreitol1drop
3100 mMEDTA1drop
420 %PEG100001reservoir
5100 mMHEPES1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97938, 0.95373
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Apr 12, 2000
RadiationMonochromator: Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979381
20.953731
ReflectionResolution: 2.6→30 Å / Num. all: 60848 / Num. obs: 56511 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 6.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.093 / % possible all: 96.3

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
MARMADdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 2826 random
Rwork0.228 --
all0.229 55982 -
obs0.229 55982 -
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13253 0 0 349 13602
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.7
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 29 Å / σ(F): 0 / Rfactor obs: 0.228 / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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