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- PDB-7wrp: Crystal Structure of pks13-ACP domain from Corynebacterium diphtheriae -

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Basic information

Entry
Database: PDB / ID: 7wrp
TitleCrystal Structure of pks13-ACP domain from Corynebacterium diphtheriae
ComponentsPolyketide synthase involved in mycolic acid biosynthesis
KeywordsRECOMBINATION / acyl-carrier protein
Function / homology4'-PHOSPHOPANTETHEINE / Polyketide synthase involved in mycolic acid biosynthesis
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.794 Å
AuthorsLiu, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structures of FadD32 and pks13-ACP domain from Corynebacterium diphtheriae.
Authors: Chen, R. / Yuan, J. / Shi, X. / Tang, W. / Liu, X.
History
DepositionJan 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyketide synthase involved in mycolic acid biosynthesis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7082
Polymers9,3501
Non-polymers3581
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-2 kcal/mol
Surface area4800 Å2
Unit cell
Length a, b, c (Å)48.886, 48.886, 111.882
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Polyketide synthase involved in mycolic acid biosynthesis


Mass: 9349.608 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Corynebacterium diphtheriae (bacteria) / References: UniProt: A0A806GVW0
#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.57 Å3/Da / Density % sol: 65.59 % / Mosaicity: 0.83 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 8
Details: 0.2 M (NH4)2SO4, 0.1 M NaAc??3H2O pH 4.6, 25% w/v PEG 4,000, VAPOR DIFFUSION, Sitting DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9784 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 1.794→50 Å / Num. obs: 13451 / % possible obs: 100 % / Redundancy: 22.2 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.028 / Rrim(I) all: 0.125 / Χ2: 1.209 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.8-1.8324.30.5916670.9540.1220.6030.917
1.83-1.8624.80.5236500.9660.1070.5341.023
1.86-1.924.40.4996350.9580.1030.511.119
1.9-1.9424.20.4666710.9590.0960.4751.113
1.94-1.9823.70.4086470.9680.0860.4171.215
1.98-2.0323.30.3546580.9780.0760.3621.289
2.03-2.0821.10.3236540.9840.0730.3321.368
2.08-2.1323.20.2846590.9830.0620.2911.427
2.13-2.223.70.2636520.9850.0560.271.383
2.2-2.2723.70.2516600.9890.0540.2561.354
2.27-2.3522.60.2286720.9910.050.2331.347
2.35-2.4421.90.2076620.9870.0460.2121.316
2.44-2.5520.30.1796650.9910.0420.1841.236
2.55-2.69220.1626680.9930.0360.1661.266
2.69-2.8621.90.1496700.9950.0330.1521.148
2.86-3.0821.20.1316810.9950.030.1351.225
3.08-3.3919.20.1186760.9970.0280.1211.175
3.39-3.8820.90.1037010.9960.0240.1060.989
3.88-4.8819.60.0957170.9970.0220.0981.185
4.88-5019.40.0957860.9970.0230.0981.131

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6c4q

6c4q


Resolution: 1.794→34.568 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2133 617 4.61 %
Rwork0.1956 12767 -
obs0.1965 13384 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.98 Å2 / Biso mean: 37.7649 Å2 / Biso min: 20.32 Å2
Refinement stepCycle: final / Resolution: 1.794→34.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms602 0 43 90 735
Biso mean--61.99 45.5 -
Num. residues----78
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.794-1.97410.2511480.22163102
1.9741-2.25970.28171310.20733147
2.2597-2.84670.23951680.22113164
2.8467-34.5680.19171700.18163354

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