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- PDB-1q9j: Structure of polyketide synthase associated protein 5 from Mycoba... -

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Basic information

Entry
Database: PDB / ID: 1q9j
TitleStructure of polyketide synthase associated protein 5 from Mycobacterium tuberculosis
ComponentsPolyketide synthase associated protein 5
KeywordsLIGASE / POLYKETIDE SYNTHASE ASSOCIATED PROTEIN / CONJUGATING ENZYME PAPA5 / Mycobacterium tuberculosis / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


phenolphthiocerol/phthiocerol/phthiodiolone dimycocerosyl transferase / Dimycocersyl phthiocerol biosynthesis / O-acyltransferase activity / DIM/DIP cell wall layer assembly / lipid biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / acyltransferase activity / lipid metabolic process
Similarity search - Function
Phthiocerol/phthiodiolone dimycocerosyl transferase, C-terminal / Phthiocerol/phthiodiolone dimycocerosyl transferase C-terminus / Nonribosomal peptide synthetase, condensation domain / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phthiocerol/phthiodiolone dimycocerosyl transferase / Phthiocerol/phthiodiolone dimycocerosyl transferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.75 Å
AuthorsBuglino, J. / Onwueme, K.C. / Quadri, L.E. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of PapA5, a Phthiocerol Dimycocerosyl Transferase from Mycobacterium tuberculosis
Authors: Buglino, J. / Onwueme, K.C. / Ferreras, J.A. / Quadri, L.E. / Lima, C.D.
History
DepositionAug 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Polyketide synthase associated protein 5
B: Polyketide synthase associated protein 5


Theoretical massNumber of molelcules
Total (without water)90,9312
Polymers90,9312
Non-polymers00
Water4,071226
1
A: Polyketide synthase associated protein 5


Theoretical massNumber of molelcules
Total (without water)45,4661
Polymers45,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polyketide synthase associated protein 5


Theoretical massNumber of molelcules
Total (without water)45,4661
Polymers45,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Polyketide synthase associated protein 5

B: Polyketide synthase associated protein 5


Theoretical massNumber of molelcules
Total (without water)90,9312
Polymers90,9312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2040 Å2
ΔGint-14 kcal/mol
Surface area35180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.982, 172.982, 80.535
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

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Components

#1: Protein Polyketide synthase associated protein 5 / papA5 / probable papA5 protein


Mass: 45465.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: PAPA5 / Plasmid: PSMT3 (MODIFIED PET28B) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P96208, UniProt: P9WIN5*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.99 Å3/Da / Density % sol: 68.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 5-10% PEG 4000, 0.2M Ammonium Acetate, 5% Glycerol, 0.02M DTT, 0.1M Sodium Citrate pH 5, pH 5., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9A10.9798
SYNCHROTRONNSLS X4A20.9798
Detector
TypeIDDetectorDate
MARRESEARCH1CCDNov 25, 2002
ADSC QUANTUM 42CCDMar 27, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. all: 35971 / Num. obs: 34892 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 70.1 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.6
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2 / Num. unique all: 3074 / % possible all: 86.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNS1.1refinement
RESOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.75→20 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1669 4.9 %RANDOM
Rwork0.236 ---
obs0.2361 33906 93.7 %-
all-36186 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.1484 Å2 / ksol: 0.304098 e/Å3
Displacement parametersBiso mean: 68.7 Å2
Baniso -1Baniso -2Baniso -3
1-5.65 Å212.19 Å20 Å2
2--5.65 Å20 Å2
3----11.31 Å2
Refine analyzeLuzzati coordinate error free: 0.51 Å / Luzzati sigma a free: 0.59 Å
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6001 0 0 226 6227
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it2.661.5
X-RAY DIFFRACTIONc_mcangle_it4.532
X-RAY DIFFRACTIONc_scbond_it3.582
X-RAY DIFFRACTIONc_scangle_it5.312.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 211 4.6 %
Rwork0.364 4418 -
obs--77.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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