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- PDB-3k6z: Crystal structure of Rv3671c protease, inactive form -

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Basic information

Entry
Database: PDB / ID: 3k6z
TitleCrystal structure of Rv3671c protease, inactive form
ComponentsPOSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE
KeywordsHYDROLASE / serine protease / disulfide / oxidative stress / 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 / peptidoglycan-based cell wall / membrane => GO:0016020 / 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: 1.75 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE
B: POSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE


Theoretical massNumber of molelcules
Total (without water)44,5722
Polymers44,5722
Non-polymers00
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-12 kcal/mol
Surface area16490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.074, 43.693, 71.468
Angle α, β, γ (deg.)90.00, 104.76, 90.00
Int Tables number5
Space group name H-MC121
Details1

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Components

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


Mass: 22286.168 Da / Num. of mol.: 2 / Fragment: UNP residues 179-397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT3772, Rv3671c / Plasmid: pET28 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.02 Å3/Da / Density % sol: 39.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Reservoir: 0.1 M Tris-HCl pH 8.5, 2.1 M ammonium phosphate monobasic, 60 mM ammonium sulfate, 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: 1.12719 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12719 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 34080 / Num. obs: 32887 / % possible obs: 96.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3564 / % possible all: 69.9

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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 3K6Y

3k6y


Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.803 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23903 1745 5 %RANDOM
Rwork0.18773 ---
all0.19024 34129 --
obs0.19024 32887 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.587 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å2-0.3 Å2
2--0.29 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 0 482 3280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222858
X-RAY DIFFRACTIONr_angle_refined_deg1.1841.9883933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8565390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.71424.57494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91615374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.951513
X-RAY DIFFRACTIONr_chiral_restr0.0770.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022191
X-RAY DIFFRACTIONr_nbd_refined0.2250.21476
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22020
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2356
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.262
X-RAY DIFFRACTIONr_mcbond_it0.7271.51999
X-RAY DIFFRACTIONr_mcangle_it0.97323183
X-RAY DIFFRACTIONr_scbond_it1.6733932
X-RAY DIFFRACTIONr_scangle_it2.5974.5750
LS refinement shellResolution: 1.754→1.799 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 77 -
Rwork0.255 1578 -
obs--63.85 %
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)Origin x (Å)Origin y (Å)Origin z (Å)
10.40340.0548-0.26670.81420.73723.79210.0266-0.0310.0454-0.0474-0.01330.0269-0.06190.1713-0.01330.05620.00680.00520.0444-0.0052-0.006-0.8723.91161.144
20.6610.1620.64991.19490.01162.09220.05460.0141-0.00620.07230.08450.08350.09380.1639-0.1390.02430.0171-0.00210.0849-0.02160.00688.8180.23827.663
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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