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- PDB-7w4u: Structure of the M. tuberculosis HtrA S407A mutant at room-temperature -

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Basic information

Entry
Database: PDB / ID: 7w4u
TitleStructure of the M. tuberculosis HtrA S407A mutant at room-temperature
ComponentsProbable serine protease HtrA1
KeywordsHYDROLASE / HtrA family of serine protease / chymotrypsin-like / Periplasm / Protein quality control and signal transduction.
Function / homology
Function and homology information


peptidase Do / peptidoglycan-based cell wall / serine-type endopeptidase activity / proteolysis / plasma membrane
Similarity search - Function
: / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases ...: / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Probable serine protease HtrA1
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGupta, A.K. / Gopal, B.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India) India
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Allosteric Determinants in High Temperature Requirement A Enzymes Are Conserved and Regulate the Population of Active Conformations.
Authors: Gupta, A.K. / Singh, K. / Patidar, Y. / Sharma, R. / Sardesai, A.A. / Reddy, G. / Gopal, B.
History
DepositionNov 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 2, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable serine protease HtrA1


Theoretical massNumber of molelcules
Total (without water)31,4581
Polymers31,4581
Non-polymers00
Water50428
1
A: Probable serine protease HtrA1

A: Probable serine protease HtrA1

A: Probable serine protease HtrA1


Theoretical massNumber of molelcules
Total (without water)94,3753
Polymers94,3753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)108.620, 108.620, 62.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

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Components

#1: Protein Probable serine protease HtrA1 / High-temperature requirement A protease


Mass: 31458.238 Da / Num. of mol.: 1 / Mutation: S407A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: htrA1, degP, htrA, Rv1223 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O06291, peptidase Do
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7.5
Details: 0.1M HEPES, 1.4M Sodium Citrate tribasic dihydrate pH 7.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→37.67 Å / Num. obs: 11713 / % possible obs: 94.86 % / Redundancy: 3.4 % / CC1/2: 0.974 / Net I/σ(I): 3.9
Reflection shellResolution: 2.3→2.383 Å / Num. unique obs: 1222 / CC1/2: 0.324

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IEO

6ieo


Resolution: 2.3→37.67 Å / Cross valid method: FREE R-VALUE / σ(F): 207.84 / Phase error: 34.78 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2069 603 5.21 %
Rwork0.1894 --
obs0.1967 11680 94.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→37.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 0 28 2041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072034
X-RAY DIFFRACTIONf_angle_d0.9912784
X-RAY DIFFRACTIONf_dihedral_angle_d6.292300
X-RAY DIFFRACTIONf_chiral_restr0.057355
X-RAY DIFFRACTIONf_plane_restr0.009373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.530.28791370.27742835X-RAY DIFFRACTION92
2.53-2.90.27262050.2422778X-RAY DIFFRACTION90
2.9-3.650.19871330.19822777X-RAY DIFFRACTION91
3.65-37.670.17511260.16262689X-RAY DIFFRACTION87

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