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- PDB-1q7c: The structure of betaketoacyl-[ACP] reductase Y151F mutant in com... -

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Basic information

Entry
Database: PDB / ID: 1q7c
TitleThe structure of betaketoacyl-[ACP] reductase Y151F mutant in complex with NADPH fragment
Components3-oxoacyl-[acyl-carrier protein] reductase
KeywordsOXIDOREDUCTASE / oxoacyl reductase / NADP+ / crystal structure
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 / fatty acid biosynthetic process / NAD binding / NADP binding / identical protein 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 / fatty acid biosynthetic process / NAD binding / NADP binding / identical protein binding / metal ion 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-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / 3-oxoacyl-[acyl-carrier-protein] reductase FabG / 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPrice, A.C. / Zhang, Y.-M. / Rock, C.O. / White, S.M.
CitationJournal: Structure / Year: 2004
Title: Cofactor-Induced Conformational Rearrangements Establish a Catalytically Competent Active Site and a Proton Relay Conduit in FabG
Authors: Price, A.C. / Zhang, Y.-M. / Rock, C.O. / White, S.M.
History
DepositionAug 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2013Group: Non-polymer description
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6334
Polymers51,1432
Non-polymers1,4912
Water1,08160
1
A: 3-oxoacyl-[acyl-carrier protein] reductase
B: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)105,2678
Polymers102,2854
Non-polymers2,9824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area16120 Å2
ΔGint-62 kcal/mol
Surface area33150 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.857, 95.857, 131.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
DetailsThe biological assembly is the tetramer formed from the dimer in the ASU by the two fold axis: -x, y, -z+1/2

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Components

#1: Protein 3-oxoacyl-[acyl-carrier protein] reductase / E.C.1.1.1.100 / betaketoacyl-[ACP] reductase / 3-ketoacyl-acyl carrier protein reductase


Mass: 25571.277 Da / Num. of mol.: 2 / Mutation: Y141F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P25716, UniProt: P0AEK2*PLUS, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.32 Å3/Da / Density % sol: 46.6 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH7.6
250 mM1dropNaCl
31 mMdithiothreitol1drop
41 mMEDTA1drop
55 mg/mlprotein1drop
620 %PEG10001reservoir
70.2 Mcalcium acetate1reservoir
80.1 MTris-HCl1reservoirpH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS / Detector: CCD / Date: Feb 5, 2003 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→65.8 Å / Num. all: 17095 / Num. obs: 17095 / % possible obs: 99.95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.61 Å / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.5 Å / Redundancy: 10.1 % / Num. measured all: 172466 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 7.9 % / Num. unique obs: 2163 / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameClassification
PROTEUM PLUSdata collection
SAINTdata reduction
LSCALEdata reduction
AMoREphasing
CNSrefinement
PROTEUM PLUSdata reduction
SAINTdata scaling
LSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→65.8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2524 1641 RANDOM
Rwork0.215 --
all0.2187 16381 -
obs0.2187 16381 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.623 Å20 Å20 Å2
2---3.703 Å20 Å2
3----2.92 Å2
Refinement stepCycle: LAST / Resolution: 2.5→65.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 62 60 3680
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0068
X-RAY DIFFRACTIONc_angle_d1.1945
X-RAY DIFFRACTIONc_angle_deg1.1945
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Rfactor Rfree: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.17

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