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- PDB-2fgg: Crystal Structure of Rv2632c -

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Basic information

Entry
Database: PDB / ID: 2fgg
TitleCrystal Structure of Rv2632c
ComponentsHypothetical protein Rv2632c/MT2708
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Rv2632c / TB target / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homologyRv1738 / Rv2632c-like / Rv2632c-like superfamily / Rv2632c-like / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein MT2708 / Uncharacterized protein Rv2632c
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsYu, M. / Bursey, E.H. / Radhakannan, T. / Segelke, B.W. / Lekin, T. / Toppani, D. / Kim, C.Y. / Kaviratne, T. / Woodruff, T. / Terwilliger, T.C. ...Yu, M. / Bursey, E.H. / Radhakannan, T. / Segelke, B.W. / Lekin, T. / Toppani, D. / Kim, C.Y. / Kaviratne, T. / Woodruff, T. / Terwilliger, T.C. / Hung, L.W. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Crystal Structure of Rv2632c
Authors: Yu, M. / Bursey, E.H. / Radhakannan, T. / Segelke, B.W. / Lekin, T. / Toppani, D. / Kim, C.Y. / Kaviratne, T. / Woodruff, T. / Terwilliger, T.C. / Hung, L.W.
History
DepositionDec 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein Rv2632c/MT2708


Theoretical massNumber of molelcules
Total (without water)11,2631
Polymers11,2631
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hypothetical protein Rv2632c/MT2708

A: Hypothetical protein Rv2632c/MT2708


Theoretical massNumber of molelcules
Total (without water)22,5262
Polymers22,5262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area3370 Å2
ΔGint-23 kcal/mol
Surface area9250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)48.054, 47.510, 94.807
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Hypothetical protein Rv2632c/MT2708


Mass: 11263.204 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: P65033, UniProt: P9WL61*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.5
Details: 0.1M Sodium Cacodylate, 11.5% Isopropanol, pH 5.5, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979259 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 9, 2005
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979259 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 4800 / % possible obs: 72.4 % / Observed criterion σ(I): 2.5 / Redundancy: 10.6 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 43.2
Reflection shellHighest resolution: 2.3 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.066 / Mean I/σ(I) obs: 43.2 / Num. unique all: 326 / Rsym value: 0.531 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.4 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / SU B: 14.663 / SU ML: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.344 / ESU R Free: 0.247
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26481 233 5.3 %RANDOM
Rwork0.22444 ---
all0.22634 ---
obs0.22634 4372 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.993 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2---0.11 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms637 0 0 14 651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021646
X-RAY DIFFRACTIONr_angle_refined_deg2.1391.962876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.947583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11824.51631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.63615110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.272156
X-RAY DIFFRACTIONr_chiral_restr0.1440.2102
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02493
X-RAY DIFFRACTIONr_nbd_refined0.2740.2281
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2413
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.221
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3570.26
X-RAY DIFFRACTIONr_mcbond_it0.7391.5429
X-RAY DIFFRACTIONr_mcangle_it1.2542667
X-RAY DIFFRACTIONr_scbond_it1.1093236
X-RAY DIFFRACTIONr_scangle_it1.8544.5209
LS refinement shellResolution: 2.305→2.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 12 -
Rwork0.261 137 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 4.0461 Å / Origin y: 14.4706 Å / Origin z: 12.5285 Å
111213212223313233
T-0.3301 Å2-0.1563 Å20.0479 Å2--0.2568 Å20.0318 Å2---0.3121 Å2
L2.5543 °2-0.1332 °2-0.9286 °2-8.545 °22.1257 °2--6.5873 °2
S-0.1126 Å °-0.0101 Å °0.099 Å °-0.6838 Å °0.0666 Å °-0.5966 Å °-0.1395 Å °0.3097 Å °0.0461 Å °

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