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- PDB-1lu4: 1.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A SECRETED MYCOBACTE... -

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Basic information

Entry
Database: PDB / ID: 1lu4
Title1.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A SECRETED MYCOBACTERIUM TUBERCULOSIS DISULFIDE OXIDOREDUCTASE HOMOLOGOUS TO E. COLI DSBE: IMPLICATIONS FOR FUNCTIONS
ComponentsSOLUBLE SECRETED ANTIGEN MPT53
KeywordsOXIDOREDUCTASE / THIOREDOXIN-LIKE FOLD / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


: / thioredoxin peroxidase activity / antioxidant activity / cell redox homeostasis / cellular response to oxidative stress / oxidoreductase activity / extracellular region / cytoplasm
Similarity search - Function
Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Soluble secreted antigen MPT53 / Soluble secreted antigen MPT53
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.12 Å
AuthorsGoulding, C.W. / Apostol, M.I. / Gleiter, S. / Parseghian, A. / Bardwell, J. / Gennaro, M. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Gram-positive DsbE Proteins Function Differently from Gram-negative DsbE Homologs: A STRUCTURE TO FUNCTION ANALYSIS OF DsbE FROM MYCOBACTERIUM TUBERCULOSIS.
Authors: Goulding, C.W. / Apostol, M.I. / Gleiter, S. / Parseghian, A. / Bardwell, J. / Gennaro, M. / Eisenberg, D.
History
DepositionMay 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: SOLUBLE SECRETED ANTIGEN MPT53


Theoretical massNumber of molelcules
Total (without water)14,6241
Polymers14,6241
Non-polymers00
Water5,783321
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.640, 60.640, 79.775
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-9002-

HOH

21A-9064-

HOH

31A-9069-

HOH

41A-9174-

HOH

Detailsmonomer in asymmetric unit

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Components

#1: Protein SOLUBLE SECRETED ANTIGEN MPT53


Mass: 14624.241 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv2878c / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-Blue cells / References: UniProt: P0A618, UniProt: P9WG65*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 2.2M ammonium sulfate, 5% isopropanol, 20% glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.5 M1dropNaCl
20.1 MTris-HCl1droppH7.4
32.2 Mammonium sulfate1reservoir
45 %isopropyl alcohol1reservoir
520 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: mirrors
RadiationMonochromator: Si III channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.12→19.99 Å / Num. all: 57093 / Num. obs: 57039 / % possible obs: 99.99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 6.8
Reflection shellResolution: 1.12→1.19 Å / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 11.4 / Num. unique all: 5671 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. obs: 45334 / % possible obs: 99.9 % / Num. measured all: 285221 / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.12→10 Å / Num. parameters: 12486 / Num. restraintsaints: 15009 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 2840 -RANDOM
Rwork0.1523 ---
all0.1526 56942 --
obs0.1526 56942 94 %-
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1328
Refinement stepCycle: LAST / Resolution: 1.12→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1076 0 0 321 1397
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.043
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0283
X-RAY DIFFRACTIONs_zero_chiral_vol0.09
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.116
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.047
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.051
X-RAY DIFFRACTIONs_approx_iso_adps0.097
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.203 / Rfactor Rwork: 0.143
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.713

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