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- PDB-3k6y: Crystal structure of Rv3671c protease from M. tuberculosis, activ... -

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Basic information

Entry
Database: PDB / ID: 3k6y
TitleCrystal structure of Rv3671c protease from M. tuberculosis, active form
ComponentsPOSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE
KeywordsHYDROLASE / serine protease / oxidative stress / disulfide / bent helix / Protease
Function / homology
Function and homology information


toxin biosynthetic process / evasion of host immune response / response to acidic pH / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / membrane => GO:0016020 / peptidoglycan-based cell wall / serine-type endopeptidase activity / proteolysis / extracellular region / plasma membrane
Similarity search - Function
Colicin V production, CvpA / : / Colicin V production protein / Peptidase S1C / Trypsin-like peptidase domain / Serine proteases, trypsin family, serine active site. / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan ...Colicin V production, CvpA / : / Colicin V production protein / Peptidase S1C / Trypsin-like peptidase domain / Serine proteases, trypsin family, serine active site. / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine protease MT3772 / Serine protease Rv3671c
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBiswas, T. / Small, J. / Vandal, O. / Ehrt, S. / Tsodikov, O.V.
CitationJournal: Structure / Year: 2010
Title: Structural insight into serine protease Rv3671c that Protects M. tuberculosis from oxidative and acidic stress.
Authors: Biswas, T. / Small, J. / Vandal, O. / Odaira, T. / Deng, H. / Ehrt, S. / Tsodikov, O.V.
History
DepositionOct 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE


Theoretical massNumber of molelcules
Total (without water)24,1411
Polymers24,1411
Non-polymers00
Water6,882382
1
A: POSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE

A: POSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE


Theoretical massNumber of molelcules
Total (without water)48,2832
Polymers48,2832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area1340 Å2
ΔGint-7 kcal/mol
Surface area20340 Å2
MethodPISA
2
A: POSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE

A: POSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE


Theoretical massNumber of molelcules
Total (without water)48,2832
Polymers48,2832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1250 Å2
ΔGint-11 kcal/mol
Surface area20420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.678, 64.678, 98.655
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-16-

HOH

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Components

#1: Protein POSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE / Serine protease


Mass: 24141.291 Da / Num. of mol.: 1 / Fragment: UNP residues 161-397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT3772, Rv3671c / Plasmid: pET19b-pps / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O69639, UniProt: P9WHR9*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: Reservoir: 0.05 M sodium acetate pH 5.25, 1.96 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.99986 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 59589 / Num. obs: 59291 / % possible obs: 99.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 10.1 % / Rmerge(I) obs: 0.067
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5868 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L1J

1l1j


Resolution: 1.3→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.293 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19928 2988 5.1 %RANDOM
Rwork0.16455 ---
all0.16628 59589 --
obs0.16628 56042 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.17 Å20 Å2
2--0.35 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1617 0 0 382 1999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221655
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9872281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1935226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.15224.18255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.38615219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.318159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021278
X-RAY DIFFRACTIONr_nbd_refined0.2150.2803
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21183
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.256
X-RAY DIFFRACTIONr_mcbond_it1.4071.51152
X-RAY DIFFRACTIONr_mcangle_it2.09621845
X-RAY DIFFRACTIONr_scbond_it4.1753539
X-RAY DIFFRACTIONr_scangle_it4.5344.5436
X-RAY DIFFRACTIONr_rigid_bond_restr3.82331691
X-RAY DIFFRACTIONr_sphericity_free4.4353382
X-RAY DIFFRACTIONr_sphericity_bonded5.14931617
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 220 -
Rwork0.238 4098 -
obs--99.91 %

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