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- PDB-3ezo: Crystal structure of acyl-carrier-protein s-malonyltransferase fr... -

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Basic information

Entry
Database: PDB / ID: 3ezo
TitleCrystal structure of acyl-carrier-protein s-malonyltransferase from burkholderia pseudomallei 1710b
ComponentsMalonyl CoA-acyl carrier protein transacylase
KeywordsTRANSFERASE / SSGCID / ACYL-CARRIER-PROTEIN S-MALONYLTRANSFERASE / BURKHOLDERIA PSEUDOMALLEI / 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 / 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 domain superfamily / Acyl transferase / Acyl transferase domain ...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 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
Malonyl CoA-acyl carrier protein transacylase
Similarity search - Component
Biological speciesBurkholderia pseudomallei 1710b (bacteria)
MethodX-RAY DIFFRACTION / molecular replacement, molecular replacement / Resolution: 2.05 Å
AuthorsSSGCID / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionOct 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 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
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


Theoretical massNumber of molelcules
Total (without water)32,9501
Polymers32,9501
Non-polymers00
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.920, 117.470, 44.530
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


Mass: 32949.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei 1710b (bacteria)
Strain: 1719B / Gene: BURKHOLDERIA PSEUDOMALLEI, BURPS1710b_2906, fabD / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q3JQ66, [acyl-carrier-protein] S-malonyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: JCSG+ SCREEN H3: 100MM BISTRIS PH 5.5, 25% PEG 3350, VAPOR DIFFUSION, TEMPERATURE 290K, pH 5.50, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 18128 / Num. obs: 18128 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 20.89 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.24
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 7.6 / Num. unique all: 1030 / % possible all: 76.4

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0046refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: molecular replacement, molecular replacement
Starting model: 1mla modified with ccp4 chainsaw

1mla


Resolution: 2.05→40.13 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.907 / SU ML: 0.107 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 914 5.1 %RANDOM
Rwork0.155 ---
all0.158 18098 --
obs0.158 18098 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å20 Å2
2---1.57 Å20 Å2
3---2.8 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 0 346 2556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222258
X-RAY DIFFRACTIONr_bond_other_d0.0010.021463
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9663079
X-RAY DIFFRACTIONr_angle_other_deg0.9833598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5455308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6824.64384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30515345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.461513
X-RAY DIFFRACTIONr_chiral_restr0.0890.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212584
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7981.51529
X-RAY DIFFRACTIONr_mcbond_other0.2121.5626
X-RAY DIFFRACTIONr_mcangle_it1.45222435
X-RAY DIFFRACTIONr_scbond_it2.5733729
X-RAY DIFFRACTIONr_scangle_it4.2324.5644
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.162 48 -
Rwork0.164 978 -
obs--76.34 %

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