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- PDB-2jax: Universal Stress Protein Rv2623 from Mycobaterium Tuberculosis -

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Basic information

Entry
Database: PDB / ID: 2jax
TitleUniversal Stress Protein Rv2623 from Mycobaterium Tuberculosis
ComponentsHYPOTHETICAL PROTEIN TB31.7
KeywordsPROTEIN BINDING / USP / UNIVERSAL STRESS PROTEIN / ATP BINDING
Function / homology
Function and homology information


dormancy entry of symbiont in host / regulation of growth / peptidoglycan-based cell wall / response to hypoxia / ATP binding / plasma membrane / cytosol
Similarity search - Function
Universal stress protein A family / UspA / Universal stress protein family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Universal stress protein MT2698 / Universal stress protein Rv2623
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.22 Å
AuthorsOberschall, A. / Bourenkov, G. / Strizhov, N. / Bartunik, H.D.
CitationJournal: To be Published
Title: Crystal Structure of Universal Stress Protein Rv2623 from Mycobacterium Tuberculosis
Authors: Oberschall, A. / Bourenkov, G. / Strizhov, N. / Bartunik, H.D.
History
DepositionNov 30, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN TB31.7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0525
Polymers33,0381
Non-polymers1,0144
Water00
1
A: HYPOTHETICAL PROTEIN TB31.7
hetero molecules

A: HYPOTHETICAL PROTEIN TB31.7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,10410
Polymers66,0752
Non-polymers2,0298
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area2760 Å2
ΔGint-19 kcal/mol
Surface area26890 Å2
MethodPQS
Unit cell
Length a, b, c (Å)102.134, 102.134, 158.068
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein HYPOTHETICAL PROTEIN TB31.7 / UNIVERSAL STRESS PROTEIN RV2623 / UNIVERSAL STRESS PROTEIN FAMILY


Mass: 33037.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET24B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2 / References: UniProt: O06189, UniProt: P9WFD7*PLUS
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
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: 3.5 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growpH: 4.6 / Details: 0.2M CACL2 0.1M NAACT PH4.6 20% ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9791
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 7, 2005 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.22→20 Å / Num. obs: 8342 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 23
Reflection shellResolution: 3.22→3.32 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 6 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.22→88.39 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.818 / Cross valid method: THROUGHOUT / ESU R Free: 0.536
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.324 388 4.7 %RANDOM
Rwork0.268 ---
obs0.27 7953 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.08 Å20 Å2
2---0.17 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 3.22→88.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 64 0 2008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222067
X-RAY DIFFRACTIONr_bond_other_d00.021927
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.9872825
X-RAY DIFFRACTIONr_angle_other_deg3.71634429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.485258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.9122.68382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76815312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1411521
X-RAY DIFFRACTIONr_chiral_restr0.1190.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022264
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02404
X-RAY DIFFRACTIONr_nbd_refined0.2890.2652
X-RAY DIFFRACTIONr_nbd_other0.2780.22148
X-RAY DIFFRACTIONr_nbtor_refined0.1940.21051
X-RAY DIFFRACTIONr_nbtor_other0.1130.2969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.250.257
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0360.21
X-RAY DIFFRACTIONr_metal_ion_refined0.5730.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined1.0670.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3460.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3090.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.761101295
X-RAY DIFFRACTIONr_mcbond_other010531
X-RAY DIFFRACTIONr_mcangle_it7.601102082
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it12.20620766
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it17.52730743
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.22→3.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 35 -
Rwork0.381 568 -
obs--99.01 %

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