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- PDB-2qc3: Crystal structure of MCAT from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 2qc3
TitleCrystal structure of MCAT from Mycobacterium tuberculosis
ComponentsMalonyl CoA-acyl carrier protein transacylase
KeywordsTRANSFERASE / malonyl-CoA:ACP transacylase / Crystal structure / Nucleophilic attack / Fatty acids biosynthesis / Mycobacterium tuberculosis
Function / homology
Function and homology information


fatty acid synthase complex / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / fatty acid biosynthetic process / cytosol
Similarity search - Function
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 domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alpha-Beta Plaits ...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 domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Malonyl CoA-acyl carrier protein transacylase / Malonyl CoA-acyl carrier protein transacylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, Z. / Huang, Y. / Ge, J. / Bartlam, M. / Wang, H. / Rao, Z.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Crystal Structure of MCAT from Mycobacterium tuberculosis Reveals Three New Catalytic Models.
Authors: Li, Z. / Huang, Y. / Ge, J. / Fan, H. / Zhou, X. / Li, S. / Bartlam, M. / Wang, H. / Rao, Z.
History
DepositionJun 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malonyl CoA-acyl carrier protein transacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0132
Polymers30,9531
Non-polymers601
Water5,783321
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.520, 48.171, 77.414
Angle α, β, γ (deg.)90.00, 98.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Malonyl CoA-acyl carrier protein transacylase / MCT


Mass: 30953.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: fabD / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P63458, UniProt: P9WNG5*PLUS, [acyl-carrier-protein] S-malonyltransferase
#2: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 0.2 M sodium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 20445 / Num. obs: 19684 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 5.6 / % possible all: 99.1

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Processing

Software
NameClassification
MAR345dtbdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NM2

1nm2


Resolution: 2.3→50 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rfree0.2379 741 -
Rwork0.1976 --
all0.202 15701 -
obs-15224 97 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.628 Å20 Å2-2.862 Å2
2---8.698 Å20 Å2
3---8.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 4 321 2485
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.16

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