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- PDB-2cuy: Crystal structure of malonyl CoA-acyl carrier protein transacylas... -

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Basic information

Entry
Database: PDB / ID: 2cuy
TitleCrystal structure of malonyl CoA-acyl carrier protein transacylase from Thermus thermophilus HB8
ComponentsMalonyl CoA-[acyl carrier protein] transacylase
KeywordsTRANSFERASE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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 speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMisaki, S. / Suzuki, K. / Kunishima, N. / Sugawara, M. / Kuroishi, C. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of malonyl CoA-acyl carrier protein transacylase from Thermus thermophilus HB8
Authors: Misaki, S. / Suzuki, K. / Kunishima, N. / Sugawara, M. / Kuroishi, C.
History
DepositionMay 31, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malonyl CoA-[acyl carrier protein] transacylase
B: Malonyl CoA-[acyl carrier protein] transacylase


Theoretical massNumber of molelcules
Total (without water)66,8572
Polymers66,8572
Non-polymers00
Water12,106672
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-11 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.907, 121.907, 114.916
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Malonyl CoA-[acyl carrier protein] transacylase


Mass: 33428.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SL77, [acyl-carrier-protein] S-malonyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 3.68 Å3/Da / Density % sol: 66.62 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7.4
Details: magnesium sulfate, HEPES, pH 7.4, EVAPORATION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1
DetectorType: RIGAKU / Detector: IMAGE PLATE / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 63134 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 14.29 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 19.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 14.44 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 6.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MLA

1mla


Resolution: 2.1→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2579 2933 RANDOM
Rwork0.2257 --
obs0.2257 57893 -
all-57893 -
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 0 672 5374

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