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- PDB-1mla: THE ESCHERICHIA COLI MALONYL-COA:ACYL CARRIER PROTEIN TRANSACYLAS... -

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Basic information

Entry
Database: PDB / ID: 1mla
TitleTHE ESCHERICHIA COLI MALONYL-COA:ACYL CARRIER PROTEIN TRANSACYLASE AT 1.5-ANGSTROMS RESOLUTION. CRYSTAL STRUCTURE OF A FATTY ACID SYNTHASE COMPONENT
ComponentsMALONYL-COENZYME A ACYL CARRIER PROTEIN TRANSACYLASE
KeywordsACYLTRANSFERASE
Function / homology
Function and homology information


[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / fatty acid biosynthetic process / cytosol
Similarity search - Function
Malonyl CoA-acyl carrier protein transacylase / Malonyl CoA-acyl carrier protein transacylase, FabD-type / : / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. ...Malonyl CoA-acyl carrier protein transacylase / Malonyl CoA-acyl carrier protein transacylase, FabD-type / : / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Malonyl CoA-acyl carrier protein transacylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsSerre, L. / Verbree, E.C. / Dauter, Z. / Stuitje, A.R. / Derewenda, Z.S.
CitationJournal: J.Biol.Chem. / Year: 1995
Title: The Escherichia coli malonyl-CoA:acyl carrier protein transacylase at 1.5-A resolution. Crystal structure of a fatty acid synthase component.
Authors: Serre, L. / Verbree, E.C. / Dauter, Z. / Stuitje, A.R. / Derewenda, Z.S.
History
DepositionJan 25, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALONYL-COENZYME A ACYL CARRIER PROTEIN TRANSACYLASE


Theoretical massNumber of molelcules
Total (without water)32,4431
Polymers32,4431
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.180, 68.180, 118.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Atom site foot note1: CIS PROLINE - PRO 52

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Components

#1: Protein MALONYL-COENZYME A ACYL CARRIER PROTEIN TRANSACYLASE / MALONYL-COA ACP TRANSACYLASE


Mass: 32443.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PMIC6 / Gene (production host): FADD / Production host: Escherichia coli (E. coli) / References: UniProt: P0AAI9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.01 MTris-HCl1drop
445 %satammonium sulfate1reservoir
50.1 MMES1reservoir
3beta-octyl glucoside1drop0.6, 1.0 or 2.0 %(w/v)

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.87 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 25, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionNum. obs: 50284 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.059
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. measured all: 343991 / Rmerge(I) obs: 0.059

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 1.5→8 Å / σ(F): 0
Details: THE MODEL WAS FIRST REFINED AT 2.0 ANGSTROMS RESOLUTION BY ONE SIMULATING ANNEALING CYCLE (X-PLOR) FOLLOWED BY ONE CYCLE OF ENERGY MINIMIZATION AND ONE CYCLE OF B-FACTORS REFINEMENT (X-PLOR). ...Details: THE MODEL WAS FIRST REFINED AT 2.0 ANGSTROMS RESOLUTION BY ONE SIMULATING ANNEALING CYCLE (X-PLOR) FOLLOWED BY ONE CYCLE OF ENERGY MINIMIZATION AND ONE CYCLE OF B-FACTORS REFINEMENT (X-PLOR). THEN THE REFINEMENT WAS EXTENDED AT 1.5 ANGSTROMS RESOLUTION USING SEVERAL CYCLES OF ENERGY MINIMIZATION AND AND B-FACTORS REFINEMENT (X-PLOR). WATER MOLECULES WERE ADDED BETWEEN EACH REFINEMENT CYCLE IN A AUTOMATIC WAY (ARP PROGRAM, LAMZIN & WILSON, ACTA CRYST., D49, 213-222 (1993)). RESIDUE SER 92 HAS A STRAINED SECONDARY STRUCTURE (PSI = -99 DEGREES, PHI = 50 DEGREES).
RfactorNum. reflection
Rwork0.184 -
obs0.184 49943
Displacement parametersBiso mean: 19.58 Å2
Refinement stepCycle: LAST / Resolution: 1.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 0 169 2409
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.45
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.591
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.69
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.0731.5
X-RAY DIFFRACTIONx_mcangle_it1.6883
X-RAY DIFFRACTIONx_scbond_it1.914
X-RAY DIFFRACTIONx_scangle_it3.0679
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_deg0.040.033
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.591
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.69
X-RAY DIFFRACTIONx_planar_d0.050.046

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