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- PDB-7w24: Structure of the M. tuberculosis HtrA N383A mutant -

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Basic information

Entry
Database: PDB / ID: 7w24
TitleStructure of the M. tuberculosis HtrA N383A mutant
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: 2.9 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 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 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)31,4311
Polymers31,4311
Non-polymers00
Water1629
1
A: Probable serine protease HtrA1

A: Probable serine protease HtrA1

A: Probable serine protease HtrA1


Theoretical massNumber of molelcules
Total (without water)94,2943
Polymers94,2943
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)106.240, 106.240, 60.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-607-

HOH

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Components

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


Mass: 31431.215 Da / Num. of mol.: 1 / Mutation: N383A
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.: 9 / 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: 2.22 Å3/Da / Density % sol: 39.28 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7.4
Details: 0.1M HEPES, 1.5M Sodium Citrate tribasic dihydrate pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→30.16 Å / Num. obs: 5544 / % possible obs: 97.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 39.61 Å2 / CC1/2: 0.98 / Net I/σ(I): 6.7
Reflection shellResolution: 2.901→3.004 Å / Num. unique obs: 559 / CC1/2: 0.91

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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: 2.9→30.16 Å / Cross valid method: FREE R-VALUE / σ(F): 28.4 / Phase error: 38.35 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2666 306 5.56 %
Rwork0.2056 --
obs0.2376 5544 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→30.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 0 0 9 1820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051833
X-RAY DIFFRACTIONf_angle_d0.9172514
X-RAY DIFFRACTIONf_dihedral_angle_d16.042286
X-RAY DIFFRACTIONf_chiral_restr0.055322
X-RAY DIFFRACTIONf_plane_restr0.008342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.650.30441480.27532677X-RAY DIFFRACTION95
3.65-30.160.29771580.20942561X-RAY DIFFRACTION90

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