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- PDB-4wsp: Racemic crystal structure of Rv1738 from Mycobacterium tuberculos... -

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Basic information

Entry
Database: PDB / ID: 4wsp
TitleRacemic crystal structure of Rv1738 from Mycobacterium tuberculosis (Form-I)
Componentsprotein DL-Rv1738
KeywordsDE NOVO PROTEIN / hypoxic response
Function / homology
Function and homology information


response to host immune response / plasma membrane / cytosol
Similarity search - Function
Rv1738 / Rv2632c-like / Rv2632c-like superfamily / Rv2632c-like / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein Rv1738
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBunker, R.D. / Mandal, K. / Kent, S.B.H. / Baker, E.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: A functional role of Rv1738 in Mycobacterium tuberculosis persistence suggested by racemic protein crystallography.
Authors: Bunker, R.D. / Mandal, K. / Bashiri, G. / Chaston, J.J. / Pentelute, B.L. / Lott, J.S. / Kent, S.B. / Baker, E.N.
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / pdbx_entity_src_syn ...citation / pdbx_entity_src_syn / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_entity_src_syn.pdbx_alt_source_flag ..._citation.journal_id_CSD / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protein DL-Rv1738
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6602
Polymers10,6241
Non-polymers351
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area6180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.130, 32.401, 58.214
Angle α, β, γ (deg.)90.000, 125.060, 90.000
Int Tables number15
Space group name H-MC12/c1
Detailsbiological unit is the same as asym.

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Components

#1: Protein protein DL-Rv1738


Mass: 10624.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria) / References: UniProt: P9WLS3
#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.: 18 / 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: 1.66 Å3/Da / Density % sol: 26 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1 microlitre of protein solution containing 9 mg/ml L-Rv1738 and 9 mg/ml D-Rv1738 in water was mixed with 1 microlitre of well solution containing 0.1 M BIS-TRIS pH 5.5, 0.2 M NaCl, 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-BM-B / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.65→47.65 Å / Num. obs: 17584 / % possible obs: 98.1 % / Redundancy: 2.8 % / Biso Wilson estimate: 49.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.041 / Net I/σ(I): 9.4 / Num. measured all: 49522
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.65-1.682.80.846123518420.8690.59796.6
9.04-47.652.20.03820.82171000.9960.03475.6

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
XDSJanuary 10, 2014data scaling
PHASER2.5.6phasing
PHENIXdev_1833refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WPY

4wpy


Resolution: 1.65→39.344 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 1239 7.33 %Random selection
Rwork0.25 15675 --
obs0.2511 16914 97.76 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.13 Å2 / Biso mean: 49.4724 Å2 / Biso min: 22.03 Å2
Refinement stepCycle: final / Resolution: 1.65→39.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms621 0 1 18 640
Biso mean--45.5 46 -
Num. residues----79
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009650
X-RAY DIFFRACTIONf_angle_d1.067884
X-RAY DIFFRACTIONf_chiral_restr0.056106
X-RAY DIFFRACTIONf_plane_restr0.006111
X-RAY DIFFRACTIONf_dihedral_angle_d14.454248
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6502-1.71630.46031360.38871745188198
1.7163-1.79440.40321450.32271760190599
1.7944-1.8890.26651260.27551747187398
1.889-2.00730.27391340.23391753188798
2.0073-2.16230.26711410.21491748188998
2.1623-2.37990.2611600.20981741190199
2.3799-2.72420.23381330.22361766189999
2.7242-3.43190.26021300.24321758188898
3.4319-39.35480.25241340.26631657179193

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