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

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Basic information

Entry
Database: PDB / ID: 4wpy
TitleRacemic crystal structure of Rv1738 from Mycobacterium tuberculosis (Form-II)
Componentsprotein DL-Rv1738
KeywordsDE NOVO PROTEIN / hypoxic response
Function / homologyRv1738 / Rv2632c-like / Rv2632c-like superfamily / Rv2632c-like / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / trifluoroacetic acid / Uncharacterized protein MT1780
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.5 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 21, 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 1.3Sep 6, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_detector ...citation / diffrn_detector / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.5Dec 27, 2023Group: 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: protein DL-Rv1738
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8303
Polymers10,6241
Non-polymers2062
Water1,51384
1
A: protein DL-Rv1738
hetero molecules

A: protein DL-Rv1738
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6606
Polymers21,2482
Non-polymers4124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)80.402, 43.989, 58.437
Angle α, β, γ (deg.)90.000, 118.440, 90.000
Int Tables number15
Space group name H-MC12/c1

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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 H37Rv (bacteria)
References: UniProt: P9WLS2
#2: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
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, 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→51.46 Å / Num. obs: 29319 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 48.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.047 / Net I/σ(I): 9.1 / Num. measured all: 107681
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
1.5-1.533.71.6520.8530314460.6971.00199.9
8.22-51.463.30.02534.76141870.9990.01695

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIXdev_1833refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: AB INITIO PHASING
Starting model: idealized 14mer polyAla helix

Resolution: 1.5→37.35 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.87 / Phase error: 23.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 2205 7.84 %Random selection
Rwork0.2281 25926 --
obs0.23 28131 99.67 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.52 Å2 / Biso mean: 31.968 Å2 / Biso min: 16.16 Å2
Refinement stepCycle: final / Resolution: 1.5→37.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms704 0 21 84 809
Biso mean--39.37 38.23 -
Num. residues----88
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011751
X-RAY DIFFRACTIONf_angle_d1.021023
X-RAY DIFFRACTIONf_chiral_restr0.051117
X-RAY DIFFRACTIONf_plane_restr0.006132
X-RAY DIFFRACTIONf_dihedral_angle_d13.616294
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.53260.53361260.478416581784100
1.5326-1.56830.42421520.421615951747100
1.5683-1.60750.43291370.367516041741100
1.6075-1.6510.37031470.351316161763100
1.651-1.69950.36851490.324216301779100
1.6995-1.75440.35981470.293216201767100
1.7544-1.81710.32191190.251516161735100
1.8171-1.88990.24451380.235416241762100
1.8899-1.97590.22411320.187716381770100
1.9759-2.080.26271520.19241597174999
2.08-2.21030.2441430.179916171760100
2.2103-2.3810.21671520.196615921744100
2.381-2.62050.22491190.188316461765100
2.6205-2.99960.21321240.200416341758100
2.9996-3.77860.20681360.192616251761100
3.7786-37.36140.22261320.22781614174699

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