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- PDB-3r97: Crystal structure of malonyl-CoA:acyl carrier protein transacylas... -

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Basic information

Entry
Database: PDB / ID: 3r97
TitleCrystal structure of malonyl-CoA:acyl carrier protein transacylase (FabD), Xoo0880, from Xanthomonas oryzae pv. oryzae KACC10331
ComponentsMalonyl CoA-ACP transacylase
KeywordsTRANSFERASE / Bacterial blight / Xoo0880 / FabD / Xanthomonas oryzae pv. oryzae KACC10331
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 / 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 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 speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNatarajan, S. / Jung, J.W. / Kang, L.W.
CitationJournal: To be Published
Title: Crystal structure of malonyl-CoA:acyl carrier protein transacylase (FabD), Xoo0880, from Xanthomonas oryzae pv. oryzae KACC10331
Authors: Natarajan, S. / Jung, J.W. / Kang, L.W.
History
DepositionMar 25, 2011Deposition site: RCSB / Processing site: PDBJ
SupersessionApr 13, 2011ID: 3EEN
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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-ACP transacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8522
Polymers32,6451
Non-polymers2071
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.425, 74.587, 98.523
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Malonyl CoA-ACP transacylase / Malonyl CoA-acyl carrier protein transacylase / FabD / Xoo0880


Mass: 32645.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria)
Strain: KACC10331 / Gene: fabD, XOO0880 / Plasmid: PET11A / Production host: Escherichia coli (E. coli)
References: UniProt: Q5H4I7, [acyl-carrier-protein] S-malonyltransferase
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M CHES pH 9.0, 1.5M Ammonium sulphate, 0.2M Sodium chloride , VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 23, 2008
RadiationMonochromator: Flat Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→49.27 Å / Num. obs: 18355 / % possible obs: 92.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.3→2.4 Å / % possible all: 88.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MLA

1mla


Resolution: 2.3→49.26 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.964 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22528 661 5.1 %RANDOM
Rwork0.1682 ---
all0.17102 12427 --
obs0.17102 12427 92.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.677 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 13 159 2465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222350
X-RAY DIFFRACTIONr_angle_refined_deg1.7911.9633204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73124.02292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96615353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6681516
X-RAY DIFFRACTIONr_chiral_restr0.1220.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211783
X-RAY DIFFRACTIONr_mcbond_it0.9641.51554
X-RAY DIFFRACTIONr_mcangle_it1.73922456
X-RAY DIFFRACTIONr_scbond_it2.9843796
X-RAY DIFFRACTIONr_scangle_it4.7774.5748
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 48 -
Rwork0.183 885 -
obs--92.28 %

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