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- PDB-1q7b: The structure of betaketoacyl-[ACP] reductase from E. coli in com... -

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Basic information

Entry
Database: PDB / ID: 1q7b
TitleThe structure of betaketoacyl-[ACP] reductase from E. coli in complex with NADP+
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 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: 2.05 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: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)105,64316
Polymers102,3494
Non-polymers3,29412
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18540 Å2
ΔGint-108 kcal/mol
Surface area32830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.748, 76.182, 99.733
Angle α, β, γ (deg.)90.00, 109.47, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsThe biological unit is the tetramer formed by chains A, B, C, and D.

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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: 25587.277 Da / Num. of mol.: 4
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.38 Å3/Da / Density % sol: 48 %
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: MACSCIENCE / Detector: IMAGE PLATE / Date: Jan 1, 2002
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 64081 / Num. obs: 64081 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.05→2.09 Å / % possible all: 90.9
Reflection
*PLUS
Redundancy: 2.8 % / Num. measured all: 306191 / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 90.9 % / Redundancy: 2.5 % / Num. unique obs: 2888 / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.26

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.221 3083 RANDOM
Rwork0.2001 --
all0.2013 61003 -
obs0.2013 61003 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.168 Å20 Å26.32 Å2
2--0.599 Å20 Å2
3----1.767 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7107 0 200 502 7809
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.7392
X-RAY DIFFRACTIONc_scbond_it1.8812
X-RAY DIFFRACTIONc_scangle_it2.72.5
Refinement
*PLUS
Rfactor Rwork: 0.2
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_deg1.18

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