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

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Basic information

Entry
Database: PDB / ID: 4pmn
TitleCrystal structure of the Mycobacterium tuberculosis Tat-secreted protein Rv2525c in complex with MES (monoclinic crystal form I)
ComponentsTat-secreted protein Rv2525c
KeywordsUNKNOWN FUNCTION / Tat secretion GH25
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
Rv2525c-like glycoside hydrolase-like domain-containing protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.44 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 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
B: Tat-secreted protein Rv2525c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7256
Polymers51,1462
Non-polymers5794
Water7,566420
1
A: Tat-secreted protein Rv2525c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8603
Polymers25,5731
Non-polymers2872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tat-secreted protein Rv2525c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8643
Polymers25,5731
Non-polymers2912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.050, 73.770, 76.065
Angle α, β, γ (deg.)90.00, 131.87, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

21A-475-

HOH

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Components

#1: Protein Tat-secreted protein Rv2525c


Mass: 25573.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: CDC 1551 / Oshkosh / Gene: MT2601 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P95028
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2 M Na formate, 100 mM sodium Acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.44→37.25 Å / Num. all: 68166 / Num. obs: 68164 / % possible obs: 92.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 19.5
Reflection shellResolution: 1.44→1.47 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 3.4 / % possible all: 58.7

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
Aimlessdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.44→37.25 Å / Cor.coef. Fo:Fc: 0.9544 / Cor.coef. Fo:Fc free: 0.9483 / SU R Cruickshank DPI: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.065 / SU Rfree Blow DPI: 0.063 / SU Rfree Cruickshank DPI: 0.062
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 3430 5.03 %RANDOM
Rwork0.162 ---
obs0.1629 68163 91.64 %-
Displacement parametersBiso mean: 16.85 Å2
Baniso -1Baniso -2Baniso -3
1--2.0391 Å20 Å2-3.606 Å2
2--3.0552 Å20 Å2
3----1.0161 Å2
Refine analyzeLuzzati coordinate error obs: 0.152 Å
Refinement stepCycle: 1 / Resolution: 1.44→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3243 0 35 420 3698
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013378HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.934610HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1503SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes73HARMONIC2
X-RAY DIFFRACTIONt_gen_planes521HARMONIC5
X-RAY DIFFRACTIONt_it3378HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.36
X-RAY DIFFRACTIONt_other_torsion2.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion410SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies12HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4191SEMIHARMONIC4
LS refinement shellResolution: 1.44→1.48 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 148 5.18 %
Rwork0.1935 2710 -
all0.195 2858 -
obs--91.64 %
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.5365-0.04-0.25011.1977-0.07830.536-0.0135-0.00660.008-0.05550.0123-0.08310.03810.02680.00120.01420.00780.01980.00410.00520.0044Chain A22.80664.0371.424
20.60360.2477-0.26411.2189-0.04470.70720.0027-0.0570.04860.0501-0.00190.04760.00330.0032-0.00080.0118-0.00390.02540.0048-0.01210.0113Chain B0.85982.12326.062
Refinement TLS groupSelection details: { B|31 - B|240 }

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