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- PDB-4pmq: Crystal structure of the Mycobacterium tuberculosis Tat-secreted ... -

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Basic information

Entry
Database: PDB / ID: 4pmq
TitleCrystal structure of the Mycobacterium tuberculosis Tat-secreted protein Rv2525c in complex with L-tartrate (orthorhombic crystal form)
ComponentsTat-secreted protein Rv2525c
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


response to antibiotic / extracellular region
Similarity search - Function
Rv2525c-like, glycoside hydrolase-like domain / Rv2525c-like, glycoside hydrolase-like domain / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Rv2525c-like glycoside hydrolase-like domain-containing protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsBellinzoni, M. / Haouz, A. / Shepard, W. / Alzari, P.M.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Structural studies suggest a peptidoglycan hydrolase function for the Mycobacterium tuberculosis Tat-secreted protein Rv2525c.
Authors: Bellinzoni, M. / Haouz, A. / Miras, I. / Magnet, S. / Andre-Leroux, G. / Mukherjee, R. / Shepard, W. / Cole, S.T. / Alzari, P.M.
History
DepositionMay 22, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Tat-secreted protein Rv2525c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5865
Polymers22,0441
Non-polymers5424
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.270, 56.770, 57.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-475-

HOH

21A-481-

HOH

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Components

#1: Protein Tat-secreted protein Rv2525c


Mass: 22043.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: CDC 1551 / Oshkosh / Gene: MT2601 / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P95028
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#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.: 163 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.3 M di-ammonium tartrate, 100 mM bis-tris propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9198 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 1.61→40.4 Å / Num. obs: 24286 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 13.23 Å2 / Rmerge(I) obs: 0.189 / Net I/σ(I): 10.7
Reflection shellResolution: 1.61→1.63 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.204 / Mean I/σ(I) obs: 1.8 / % possible all: 95.7

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PMN

4pmn


Resolution: 1.61→18.26 Å / Cor.coef. Fo:Fc: 0.9507 / Cor.coef. Fo:Fc free: 0.9349 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.09 / SU Rfree Blow DPI: 0.088 / SU Rfree Cruickshank DPI: 0.086
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 1226 5.1 %RANDOM
Rwork0.1659 ---
obs0.1675 24057 100 %-
Displacement parametersBiso mean: 12.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.0827 Å20 Å20 Å2
2--0.9795 Å20 Å2
3----2.0622 Å2
Refine analyzeLuzzati coordinate error obs: 0.159 Å
Refinement stepCycle: 1 / Resolution: 1.61→18.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 36 163 1763
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011643HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.952240HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d725SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes35HARMONIC2
X-RAY DIFFRACTIONt_gen_planes260HARMONIC5
X-RAY DIFFRACTIONt_it1643HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.05
X-RAY DIFFRACTIONt_other_torsion2.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion206SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2054SEMIHARMONIC4
LS refinement shellResolution: 1.61→1.68 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2334 143 4.94 %
Rwork0.2147 2753 -
all0.2156 2896 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -11.6233 Å / Origin y: 13.9861 Å / Origin z: -15.8108 Å
111213212223313233
T-0.0393 Å20.0057 Å20.0043 Å2--0.0561 Å2-0.0049 Å2---0.0092 Å2
L0.3422 °20.0687 °20.0496 °2-0.3129 °20.0061 °2--0.4568 °2
S0.0136 Å °-0.0117 Å °0.0095 Å °0.0256 Å °-0.0103 Å °0.0215 Å °-0.0203 Å °-0.0118 Å °-0.0033 Å °
Refinement TLS groupSelection details: { A|37 - A|240 }

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