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- PDB-3g87: Crystal structure of malonyl CoA-acyl carrier protein transacylas... -

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Basic information

Entry
Database: PDB / ID: 3g87
TitleCrystal structure of malonyl CoA-acyl carrier protein transacylase from Burkholderia pseudomallei using dried seaweed as nucleant or protease
ComponentsMalonyl CoA-acyl carrier protein transacylase
KeywordsTRANSFERASE / SSGCID / NIAID / deCODE biostructures / dried seaweed / Acyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity
Similarity search - Function
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 ...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
[acyl-carrier-protein] S-malonyltransferase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of malonyl CoA-acyl carrier protein transacylase from Burkholderia pseudomallei using dried seaweed as nucleant or protease
Authors: Edwards, T.E. / Staker, B.L. / Christensen, J. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionFeb 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malonyl CoA-acyl carrier protein transacylase


Theoretical massNumber of molelcules
Total (without water)42,5181
Polymers42,5181
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.495, 69.196, 83.202
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Malonyl CoA-acyl carrier protein transacylase


Mass: 42517.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Expressed with an N-terminal His tag, which was removed with 3C protease leaving GPGS at the N-terminus of the protein
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: 102, 76, 818, BURPS1710b_A2616, pedD / Production host: Escherichia coli (E. coli)
References: UniProt: Q3JF88, [acyl-carrier-protein] S-malonyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 1.95 Å3/Da / Density % sol: 36.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 24.5 mg/mL protein, JCSG+ screen well h6; used dried seaweed as nucleant or protease as described by Thakur et al PLOS one 2007, 2, e1091 and D'Arcy et al Acta Cryst D 2003, 59, 1343; 0.1 M ...Details: 24.5 mg/mL protein, JCSG+ screen well h6; used dried seaweed as nucleant or protease as described by Thakur et al PLOS one 2007, 2, e1091 and D'Arcy et al Acta Cryst D 2003, 59, 1343; 0.1 M BisTris pH 5.5, 17% PEG 10,000, 0.1 M NH4OAC; Crystal ID 201868h6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 5, 2009
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. obs: 14632 / % possible obs: 95.4 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.151 / Χ2: 1.524 / Net I/σ(I): 9.025
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.384.60.49814881.18199.2
2.38-2.484.60.45814741.273198.3
2.48-2.594.70.39214671.349197.8
2.59-2.734.70.36214731.341196.9
2.73-2.94.60.33214481.517196.5
2.9-3.124.70.21514551.551196
3.12-3.4450.12914601.584195.1
3.44-3.934.80.10114501.566194.3
3.93-4.9550.07714621.492193.4
4.95-504.60.09614552.402187.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MLA

1mla


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.2 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.809 / SU B: 6.768 / SU ML: 0.164 / SU R Cruickshank DPI: 0.38 / SU Rfree: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.38 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.254 708 4.9 %RANDOM
Rwork0.21 ---
obs0.212 14506 94.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.91 Å2 / Biso mean: 25.16 Å2 / Biso min: 5.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2---0.03 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 0 191 2406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212258
X-RAY DIFFRACTIONr_angle_refined_deg1.741.9513062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3795289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17123.364110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.06315354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2821521
X-RAY DIFFRACTIONr_chiral_restr0.1080.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211760
X-RAY DIFFRACTIONr_mcbond_it0.961.51440
X-RAY DIFFRACTIONr_mcangle_it1.7622288
X-RAY DIFFRACTIONr_scbond_it2.983818
X-RAY DIFFRACTIONr_scangle_it4.7414.5774
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 48 -
Rwork0.218 1055 -
all-1103 -
obs--99.1 %

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