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- PDB-3ptw: CRYSTAL STRUCTURE OF malonyl CoA-acyl carrier protein transacylas... -

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Basic information

Entry
Database: PDB / ID: 3ptw
TitleCRYSTAL STRUCTURE OF malonyl CoA-acyl carrier protein transacylase from Clostridium perfringens Atcc 13124
ComponentsMalonyl CoA-acyl carrier protein transacylase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / NYSGRC / PSI-Biology
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 / Malonyl CoA-acyl carrier protein transacylase
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsMalashkevich, V.N. / Toro, R. / Ramagopal, U. / Seidel, R. / Foti, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF malonyl CoA-acyl carrier protein transacylase from Clostridium perfringens Atcc 13124
Authors: Malashkevich, V.N. / Toro, R. / Ramagopal, U. / Seidel, R. / Foti, R. / Almo, S.C.
History
DepositionDec 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)37,1291
Polymers37,1291
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.703, 87.075, 87.353
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: 37128.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: ATCC 13124 / Gene: fabD, CPF_1325 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: Q0TRG9, UniProt: A0A0H2YQN3*PLUS, [acyl-carrier-protein] S-malonyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.03 Å3/Da / Density % sol: 39.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 18007 / % possible obs: 98.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.1 / Χ2: 1.019 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.145.60.7437970.66988.9
2.14-2.1860.6748370.68693.4
2.18-2.226.30.8928710.78297
2.22-2.266.20.3898850.74898.2
2.26-2.316.80.8989020.899.7
2.31-2.376.90.4678940.74399.8
2.37-2.427.10.3838850.75399.8
2.42-2.497.10.3529200.77599.9
2.49-2.567.10.2948900.772100
2.56-2.657.20.2629170.77899.9
2.65-2.747.10.2278950.81999.9
2.74-2.8570.189090.87899.8
2.85-2.986.70.1418920.946100
2.98-3.146.60.1159271.05699.9
3.14-3.336.50.0859221.13999.8
3.33-3.596.30.0749161.38799.9
3.59-3.955.80.0648371.57888.9
3.95-4.526.10.0559231.635100
4.52-5.76.10.0539631.61399.9
5.7-506.40.05110251.87999.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.73 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.68 Å
Translation2.5 Å43.68 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.85 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2437 / WRfactor Rwork: 0.196 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.78 / SU B: 15.113 / SU ML: 0.178 / SU R Cruickshank DPI: 0.2824 / SU Rfree: 0.2175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 907 5.1 %RANDOM
Rwork0.2176 ---
obs0.2201 17839 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 68.73 Å2 / Biso mean: 38.722 Å2 / Biso min: 17.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 0 90 2506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222448
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9913290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4745315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.30326.7100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.86615476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.297155
X-RAY DIFFRACTIONr_chiral_restr0.0890.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211776
X-RAY DIFFRACTIONr_mcbond_it0.6693.51561
X-RAY DIFFRACTIONr_mcangle_it3.145502509
X-RAY DIFFRACTIONr_scbond_it8.07550887
X-RAY DIFFRACTIONr_scangle_it0.6754.5781
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 69 -
Rwork0.296 1063 -
all-1132 -
obs--86.88 %
Refinement TLS params.Method: refined / Origin x: -2.3665 Å / Origin y: -7.3057 Å / Origin z: 12.34 Å
111213212223313233
T0.0606 Å20.0142 Å2-0.0289 Å2-0.0149 Å2-0.01 Å2--0.0204 Å2
L0.998 °2-0.0244 °2-0.2588 °2-0.8918 °2-0.6328 °2--1.0918 °2
S-0.0017 Å °0.0132 Å °0.0386 Å °-0.0654 Å °0.0066 Å °0.0451 Å °0.0488 Å °0.0038 Å °-0.0048 Å °

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