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- PDB-4o6g: Rv3902c from M. tuberculosis -

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Basic information

Entry
Database: PDB / ID: 4o6g
TitleRv3902c from M. tuberculosis
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / TB Structural Genomics Consortium / TBSGC
Function / homologyImmunity protein IFT-like / Immunity protein 61 / Immunity factor for TNT
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsReddy, B.G. / Moates, D.B. / Kim, H. / Green, T.J. / Kim, C. / Terwilliger, T.J. / Delucas, L.J. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: 1.55 angstrom resolution X-ray crystal structure of Rv3902c from Mycobacterium tuberculosis.
Authors: Reddy, B.G. / Moates, D.B. / Kim, H.B. / Green, T.J. / Kim, C.Y. / Terwilliger, T.C. / Delucas, L.J.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)19,5471
Polymers19,5471
Non-polymers00
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.819, 91.819, 54.231
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Uncharacterized protein


Mass: 19546.965 Da / Num. of mol.: 1 / Fragment: Rv3902c
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC BAA-935 / AF2122/97 / Gene: Mb3932c, MT4020, Rv3902c / Production host: Escherichia coli (E. coli) / References: UniProt: L7N519
#2: Water ChemComp-HOH / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein Concentration 25mg/ml, 1.5M ammonium sulphate, and 200mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→39.76 Å / Num. all: 37938 / Num. obs: 37938 / % possible obs: 100 % / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX(phenix.refine: 1.8.2_1309)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Bromide Soaked SAD Crystal Structure

Resolution: 1.55→39.759 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 16.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1767 1985 5.24 %
Rwork0.1654 --
obs0.166 37909 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→39.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 0 226 1600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061433
X-RAY DIFFRACTIONf_angle_d0.9681945
X-RAY DIFFRACTIONf_dihedral_angle_d12.103527
X-RAY DIFFRACTIONf_chiral_restr0.068213
X-RAY DIFFRACTIONf_plane_restr0.004252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5501-1.58880.29091450.26392565X-RAY DIFFRACTION100
1.5888-1.63180.22861440.2272522X-RAY DIFFRACTION100
1.6318-1.67980.2071420.19952555X-RAY DIFFRACTION100
1.6798-1.7340.20021410.1842568X-RAY DIFFRACTION100
1.734-1.7960.19661390.1792537X-RAY DIFFRACTION100
1.796-1.86790.18151380.16522580X-RAY DIFFRACTION100
1.8679-1.95290.17541400.15262536X-RAY DIFFRACTION100
1.9529-2.05590.16061410.14372573X-RAY DIFFRACTION100
2.0559-2.18470.17411400.15532561X-RAY DIFFRACTION100
2.1847-2.35340.19641420.14912550X-RAY DIFFRACTION100
2.3534-2.59020.17271430.15712576X-RAY DIFFRACTION100
2.5902-2.96490.18471410.16892588X-RAY DIFFRACTION100
2.9649-3.7350.16691440.15392566X-RAY DIFFRACTION100
3.735-39.7720.15411450.16952647X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.249-0.69120.43661.0449-1.55554.4077-0.0049-0.156-0.2625-0.09860.23930.22720.8789-0.4129-0.1750.13510.0529-0.00570.1550.04450.151825.059526.931742.7732
22.4133-0.2535-0.1443.6753-0.36491.1173-0.0127-0.0269-0.03950.00440.0674-0.13720.19790.1835-0.05420.12160.0872-0.00980.1501-0.01470.095836.538128.533742.8209
31.62030.06780.99320.44070.06144.0680.16840.0684-0.1129-0.04970.04130.01220.37520.0546-0.17070.13760.073-0.01940.15380.01510.124328.807733.197932.8131
42.7210.80481.75331.45650.60284.3013-0.07630.2960.2177-0.06890.02410.0749-0.30910.40990.07880.06430.03930.02350.20530.00130.154938.512942.944331.4215
53.54381.31532.23511.12140.50753.2921-0.05940.06570.3847-0.09620.03130.2077-0.3092-0.06770.00770.12620.06280.01460.14650.01090.157730.728642.852632.6054
65.9238-0.61460.63723.42740.05420.09580.10520.7353-0.0642-0.35340.2492-0.26490.03090.4715-0.15710.17710.0886-0.01410.3229-0.05530.133728.759337.736716.6829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 73 )
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 92 )
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 127 )
5X-RAY DIFFRACTION5chain 'A' and (resid 128 through 161 )
6X-RAY DIFFRACTION6chain 'A' and (resid 162 through 174 )

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