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- PDB-2c07: Oxoacyl-ACP reductase of Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 2c07
TitleOxoacyl-ACP reductase of Plasmodium falciparum
Components3-OXOACYL-(ACYL-CARRIER PROTEIN) REDUCTASE
KeywordsOXIDOREDUCTASE / FABG / SHORT-CHAIN ALCOHOL REDUCTASE / FATTY ACID BIOSYNTHESIS / APICOPLAST / KETOACYL-ACP REDUCTASE
Function / homology
Function and homology information


Fatty acyl-CoA biosynthesis / acetoacetyl-CoA reductase activity / : / : / : / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NADPH binding / fatty acid biosynthetic process / NAD binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / 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
Oxoacyl-ACP reductase / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsUrch, J.E. / Wickramasinghe, S.R. / Inglis, K.A. / Muller, S. / Fairlamb, A.H. / van Aalten, D.M.F.
CitationJournal: Biochem.J. / Year: 2006
Title: Kinetic, Inhibition and Structural Studies on 3-Oxoacyl-Acp Reductase from Plasmodium Falciparum, a Key Enzyme in Fatty Acid Biosynthesis.
Authors: Wickramasinghe, S.R. / Inglis, K.A. / Urch, J.E. / Muller, S. / Van Aalten, D.M.F. / Fairlamb, A.H.
History
DepositionAug 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: 3-OXOACYL-(ACYL-CARRIER PROTEIN) REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6312
Polymers31,5351
Non-polymers961
Water3,315184
1
A: 3-OXOACYL-(ACYL-CARRIER PROTEIN) REDUCTASE
hetero molecules

A: 3-OXOACYL-(ACYL-CARRIER PROTEIN) REDUCTASE
hetero molecules

A: 3-OXOACYL-(ACYL-CARRIER PROTEIN) REDUCTASE
hetero molecules

A: 3-OXOACYL-(ACYL-CARRIER PROTEIN) REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,5248
Polymers126,1394
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
crystal symmetry operation7_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)73.121, 73.121, 100.176
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-2112-

HOH

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Components

#1: Protein 3-OXOACYL-(ACYL-CARRIER PROTEIN) REDUCTASE / OXOACYL-ACP REDUCTASE


Mass: 31534.859 Da / Num. of mol.: 1 / Fragment: 54-C TERMINUS, RESIDUES 54-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: 3D7 / Plasmid: PJC40 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODON PLUS RIL
References: UniProt: Q86RB1, UniProt: Q8I2S7*PLUS, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS OF THIS GENBANK ENTRY ARE ALSO AUTHORS OF THE STRUCTURAL DATA. IN THIS GENBANK ENTRY, ...THE AUTHORS OF THIS GENBANK ENTRY ARE ALSO AUTHORS OF THE STRUCTURAL DATA. IN THIS GENBANK ENTRY, RESIDUE 58 HAS BEEN ENTERED INCORRECTLY AS A HISTIDINE NOT A TYROSINE. A CHECK OF THE DNA SEQUENCING BY THESE AUTHORS SUGGESTS RESIDUE 58 IS A TYROSINE AS OBSERVED BY THE STRUCTURE. WE ARE CURRENTLY WRITING TO NCBI TO AMEND THE Q86RB1_PLAF7 AND ITS CORRESPONDING NUCLEOTIDE ENTRY.

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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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growpH: 6
Details: 35% (V/V) 2-METHYL-2, 4-PENTANEDIOL, 100MM MES, PH6.0 200MM LI2SO4, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 259420 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 36.9
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q7B

1q7b


Resolution: 1.5→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3225021.62 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THIS ENTRY CONTAINS ATOMS WHOSE B- FACTORS HAVE BEEN REFINED BUT HAVE AN OCCUPANCY OF 0.00.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 907 2.1 %RANDOM
Rwork0.202 ---
obs0.202 44089 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.5243 Å2 / ksol: 0.344853 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1881 0 5 184 2070
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.821.5
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scbond_it3.062
X-RAY DIFFRACTIONc_scangle_it4.282.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 152 2.1 %
Rwork0.267 7047 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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