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

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Basic information

Entry
Database: PDB / ID: 4pmo
TitleCrystal structure of the Mycobacterium tuberculosis Tat-secreted protein Rv2525c, 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
FORMIC ACID / Rv2525c-like glycoside hydrolase-like domain-containing protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)52,10924
Polymers50,9592
Non-polymers1,15122
Water6,666370
1
A: Tat-secreted protein Rv2525c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,10113
Polymers25,4791
Non-polymers62112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tat-secreted protein Rv2525c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,00911
Polymers25,4791
Non-polymers52910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.442, 73.679, 74.415
Angle α, β, γ (deg.)90.00, 130.85, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-429-

HOH

21A-471-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 30 - 240 / Label seq-ID: 24 - 234

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Tat-secreted protein Rv2525c


Mass: 25479.346 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 / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P95028
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.02 Å3/Da / Density % sol: 39.21 %
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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.33→37.61 Å / Num. obs: 90524 / % possible obs: 97.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.9
Reflection shellResolution: 1.33→1.35 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.8 / % possible all: 75.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PMN

4pmn


Resolution: 1.33→36.95 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.872 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16493 4528 5 %RANDOM
Rwork0.1495 ---
obs0.15027 85995 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.776 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.32 Å2
2---0.35 Å2-0 Å2
3---0.37 Å2
Refinement stepCycle: 1 / Resolution: 1.33→36.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 72 370 3620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193380
X-RAY DIFFRACTIONr_bond_other_d0.0050.023094
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.9334592
X-RAY DIFFRACTIONr_angle_other_deg1.10637093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1995443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.26723.288146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.71115480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5571520
X-RAY DIFFRACTIONr_chiral_restr0.1090.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213994
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02850
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0170.6841710
X-RAY DIFFRACTIONr_mcbond_other1.0170.6841711
X-RAY DIFFRACTIONr_mcangle_it1.6511.0242140
X-RAY DIFFRACTIONr_mcangle_other1.6511.0242141
X-RAY DIFFRACTIONr_scbond_it1.8060.8611670
X-RAY DIFFRACTIONr_scbond_other1.7420.8481650
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7161.1982441
X-RAY DIFFRACTIONr_long_range_B_refined5.2446.794141
X-RAY DIFFRACTIONr_long_range_B_other5.0716.1893980
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12322 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.33→1.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 279 -
Rwork0.35 5002 -
obs--77.28 %
Refinement TLS params.

T12: 0.0029 Å2 / 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)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.3541-0.04370.23620.7778-0.03860.43470.00720.0051-0.0114-0.04310.0080.0111-0.0081-0.0168-0.01520.042-0.04370.0018-0.0020.0488Chain A-22.8728.9261.465
20.37830.04950.21960.8617-0.0290.4286-0.0136-0.0311-0.00470.0070.0045-0.0289-0.0041-0.00240.00910.0366-0.04650.0036-0.00130.0615Chain B-0.825-8.93126.008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B30 - 240
2X-RAY DIFFRACTION2B30 - 240

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