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- PDB-4rr5: The crystal structure of Synechocystis sp. PCC 6803 Malonyl-CoA: ... -

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Basic information

Entry
Database: PDB / ID: 4rr5
TitleThe crystal structure of Synechocystis sp. PCC 6803 Malonyl-CoA: ACP Transacylase
ComponentsMalonyl CoA-acyl carrier protein transacylase
KeywordsTRANSFERASE / hydrolase
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
ACETATE ION / Malonyl CoA-acyl carrier protein transacylase
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.427 Å
AuthorsLiu, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Structural and biochemical characterization of MCAT from photosynthetic microorganism Synechocystis sp. PCC 6803 reveal its stepwise catalytic mechanism
Authors: Liu, Y. / Feng, Y. / Wang, Y. / Li, X. / Cao, X. / Xue, S.
History
DepositionNov 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Malonyl CoA-acyl carrier protein transacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5752
Polymers31,5161
Non-polymers591
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.043, 148.646, 40.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 31515.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Gene: fabD, slr2023 / Production host: Escherichia coli (E. coli)
References: UniProt: P73242, [acyl-carrier-protein] S-malonyltransferase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M ammonium acetate, 0.1M sodium acetate trihydrate pH 4.6, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 6, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. obs: 15645 / % possible obs: 90.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.42-2.66189.8
2.66-3.05190.4
3.05-5.54191.2
5.54-50199.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MLA

1mla


Resolution: 2.427→41.345 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 26.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 465 4.82 %RANDOM
Rwork0.1829 ---
obs0.1864 9656 92.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.427→41.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2206 0 4 63 2273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082245
X-RAY DIFFRACTIONf_angle_d1.1143046
X-RAY DIFFRACTIONf_dihedral_angle_d14.593814
X-RAY DIFFRACTIONf_chiral_restr0.039353
X-RAY DIFFRACTIONf_plane_restr0.005399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4273-2.77850.33441630.2399287090
2.7785-3.50030.28471450.201296891
3.5003-41.35050.21051570.1564335397

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