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- PDB-7w4r: Structure of the M. tuberculosis HtrA N269A mutant at room-temperature -

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Basic information

Entry
Database: PDB / ID: 7w4r
TitleStructure of the M. tuberculosis HtrA N269A mutant at room-temperature
ComponentsProbable serine protease HtrA1
KeywordsHYDROLASE / HtrA family of serine protease / chymotrypsin-like / Periplasm / Protein quality control / signal transduction and room temperature data.
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 / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Probable serine protease HtrA1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.701 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)32,4791
Polymers32,4791
Non-polymers00
Water45025
1
A: Probable serine protease HtrA1

A: Probable serine protease HtrA1

A: Probable serine protease HtrA1


Theoretical massNumber of molelcules
Total (without water)97,4383
Polymers97,4383
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
Buried area3950 Å2
ΔGint-14 kcal/mol
Surface area35480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.500, 108.500, 62.240
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-625-

HOH

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Components

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


Mass: 32479.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / 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.: 25 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
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 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.701→37.5 Å / Num. obs: 7485 / % possible obs: 99.8 % / Redundancy: 2.5 % / CC1/2: 0.967 / Net I/σ(I): 6
Reflection shellResolution: 2.701→2.797 Å / Num. unique obs: 751 / CC1/2: 0.263

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.18.2_3874: ???refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IEO

6ieo


Resolution: 2.701→37.5 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 24.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2238 415 5.54 %
Rwork0.1682 --
obs0.1714 7485 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.701→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 0 25 2059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032054
X-RAY DIFFRACTIONf_angle_d0.5522809
X-RAY DIFFRACTIONf_dihedral_angle_d21.279300
X-RAY DIFFRACTIONf_chiral_restr0.05359
X-RAY DIFFRACTIONf_plane_restr0.003375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.701-3.090.3392740.22242431X-RAY DIFFRACTION100
3.09-3.890.23551920.16992306X-RAY DIFFRACTION100
3.9-37.50.18891490.14212336X-RAY DIFFRACTION100

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