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- PDB-3lt3: Crystal structure of Rv3671c from M. tuberculosis H37Rv, Ser343Al... -

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Basic information

Entry
Database: PDB / ID: 3lt3
TitleCrystal structure of Rv3671c from M. tuberculosis H37Rv, Ser343Ala mutant, inactive form
ComponentsPOSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE
KeywordsHYDROLASE / serine protease / H37Rv / HtrA / 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 H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionFeb 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)44,1442
Polymers44,1442
Non-polymers00
Water2,918162
1
A: POSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE


Theoretical massNumber of molelcules
Total (without water)22,0721
Polymers22,0721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: POSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE


Theoretical massNumber of molelcules
Total (without water)22,0721
Polymers22,0721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: POSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE

B: POSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE


Theoretical massNumber of molelcules
Total (without water)44,1442
Polymers44,1442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_456x-1,y,z+11
Buried area1810 Å2
ΔGint-13 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.603, 44.207, 53.356
Angle α, β, γ (deg.)101.68, 97.56, 105.05
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 22071.947 Da / Num. of mol.: 2 / Fragment: Rv3671c (179-397) / Mutation: S343A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
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 / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.13 Å3/Da / Density % sol: 42.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl, 2.1 M ammonium phosphate monobasic, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.002 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.002 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 19845 / Num. obs: 18853 / % possible obs: 95 % / Observed criterion σ(I): 3.8 / Redundancy: 2.1 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 22.6
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 3.8 / % possible all: 84.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K6Z
Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.888 / SU B: 15.469 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27628 1018 5.1 %RANDOM
Rwork0.22654 ---
all0.22909 19845 --
obs0.22909 18853 94.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.377 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.5 Å21.89 Å2
2--0.21 Å21.06 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 0 162 2984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222882
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9261.9863971
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4335398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66224.20588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12815362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.2321513
X-RAY DIFFRACTIONr_chiral_restr0.0540.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022201
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1710.21342
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21990
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0810.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0650.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2791.52041
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.4123245
X-RAY DIFFRACTIONr_scbond_it0.4713909
X-RAY DIFFRACTIONr_scangle_it0.8264.5726
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 61 -
Rwork0.265 1188 -
obs--82.01 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.1303-0.2573-0.65214.4482-0.11592.4543-0.01-0.04150.02150.05860.08410.2191-0.0123-0.092-0.0741-0.16050.0161-0.0279-0.09240.0029-0.1055-0.7867-0.27351.2208
22.99391.4471-1.99242.9002-0.87574.89590.1272-0.25040.0959-0.0327-0.097-0.0935-0.00020.5868-0.0301-0.18940.013-0.0325-0.03980.0055-0.128823.80316.1056-25.6716
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 500
2X-RAY DIFFRACTION2B1 - 500

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