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- PDB-4pws: Crystal structure of secreted proline rich antigen MTC28 (Rv0040c... -

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Basic information

Entry
Database: PDB / ID: 4pws
TitleCrystal structure of secreted proline rich antigen MTC28 (Rv0040c) at 2.15 A with bound chloride from Mycobacterium tuberculosis
ComponentsProline-rich 28 kDa antigen
KeywordsIMMUNE SYSTEM / Probable lipoprotein LpqN
Function / homologyLipoprotein LpqN/LpqT-like / Probable lipoprotein LpqN / extracellular region / Proline-rich 28 kDa antigen / Proline-rich 28 kDa antigen
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKundu, P. / Biswas, R. / Mukherjee, S. / Reinhard, L. / Mueller-dieckmann, J. / Weiss, M.S. / Das, A.K.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structure-based Epitope Mapping of Mycobacterium tuberculosis Secretary Antigen MTC28
Authors: Kundu, P. / Biswas, R. / Mukherjee, S. / Reinhard, L. / Dutta, A. / Mueller-Dieckmann, J. / Weiss, M.S. / Pal, N.K. / Das, A.K.
History
DepositionMar 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Data collection
Revision 1.2Jan 11, 2017Group: Database references
Revision 1.3Dec 18, 2019Group: Data collection / Database references / Category: reflns_shell / struct_ref_seq_dif
Item: _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.4Nov 8, 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: Proline-rich 28 kDa antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9352
Polymers29,9001
Non-polymers351
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.410, 101.410, 67.690
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Proline-rich 28 kDa antigen


Mass: 29899.729 Da / Num. of mol.: 1 / Fragment: UNP residues 32-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT0046, mtc28, MTCY21D4.03c, Rv0040c / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P0A5Q6, UniProt: P9WIM9*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.36 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.25M Sodium Chloride, 100mM Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.771 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.771 Å / Relative weight: 1
ReflectionHighest resolution: 2.15 Å / Num. obs: 42287 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.257 Å2 / Rmerge(I) obs: 0.104 / Χ2: 1.037 / Net I/σ(I): 14.19
Reflection shell

Rmerge(I) obs: 1.171 / Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.15-2.210.7411.9817342312931171.29199.6
2.21-2.270.82.5117163307230661.08899.8
2.27-2.330.8643.0916567295329470.89699.8
2.33-2.40.8913.6316242287728750.78999.9
2.4-2.480.9514.4315968282928050.61299.2
2.48-2.570.9555.6815173267026660.4899.9
2.57-2.670.9727.3815036263226300.35199.9
2.67-2.780.9839.4114381251525110.26199.8
2.78-2.90.98810.9913952243224280.21499.8
2.9-3.040.99214.0113031227822760.15699.9
3.04-3.210.99618.0212457219921950.11199.8
3.21-3.40.99621.0511684206920680.09100
3.4-3.630.99725.4310705193519300.07199.7
3.63-3.930.99729.879863182318230.058100
3.93-4.30.99832.589544164416440.051100
4.3-4.810.99936.098774151315120.04499.9
4.81-5.550.999367936133513350.043100
5.55-6.80.99935.646705112411230.04299.9
6.8-9.620.99940.2351348648640.035100
9.620.99941.8126864794720.03398.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OL4

4ol4


Resolution: 2.15→43.95 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2125 / WRfactor Rwork: 0.1852 / FOM work R set: 0.8703 / SU B: 3.278 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1242 / SU Rfree: 0.1213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 1132 5.1 %RANDOM
Rwork0.1892 ---
obs0.1905 22143 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.54 Å2 / Biso mean: 40.735 Å2 / Biso min: 20.33 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å21.03 Å20 Å2
2--1.03 Å20 Å2
3----3.36 Å2
Refinement stepCycle: LAST / Resolution: 2.15→43.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1341 0 1 47 1389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0191371
X-RAY DIFFRACTIONr_bond_other_d0.0010.021299
X-RAY DIFFRACTIONr_angle_refined_deg2.4761.9521875
X-RAY DIFFRACTIONr_angle_other_deg1.06132982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8885175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.9923.96658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.30915209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.269159
X-RAY DIFFRACTIONr_chiral_restr0.1820.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211563
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02306
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 72 -
Rwork0.248 1536 -
all-1608 -
obs--99.69 %

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