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- PDB-5zvj: Crystal structure of HtrA1 from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 5zvj
TitleCrystal structure of HtrA1 from Mycobacterium tuberculosis
ComponentsSerine protease
KeywordsHYDROLASE / HtrA / Mycobacterium / PDZ / Protease
Function / homology
Function and homology information


peptidase Do / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / membrane => GO:0016020 / 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
Serine protease / Probable serine protease HtrA1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKhundrakpam, H.S. / Yadav, S. / Kumar, D. / Biswal, B.K.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: The crystal structure of an essential high-temperature requirement protein HtrA1 (Rv1223) from Mycobacterium tuberculosis reveals its unique features.
Authors: Singh, K.H. / Yadav, S. / Kumar, D. / Biswal, B.K.
History
DepositionMay 10, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 5, 2018ID: 5XDY
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 25, 2019Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 22, 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9882
Polymers34,8661
Non-polymers1221
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint2 kcal/mol
Surface area14470 Å2
Unit cell
Length a, b, c (Å)135.391, 135.391, 45.852
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Serine protease


Mass: 34865.910 Da / Num. of mol.: 1 / Mutation: S387A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: htrA, SAMEA2682835_04373 / Production host: Mycobacterium smegmatis (bacteria)
References: UniProt: A0A1K3KH35, UniProt: O06291*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases, peptidase Do
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.49 Å3/Da / Density % sol: 64.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, PEG2000, Ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.7→42.7 Å / Num. obs: 12591 / % possible obs: 93.8 % / Redundancy: 9.3 % / Biso Wilson estimate: 40.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.041 / Net I/σ(I): 17.2
Reflection shellResolution: 2.7→2.84 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y8T

1y8t


Resolution: 2.7→42.7 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 12.301 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.477 / ESU R Free: 0.305 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24975 692 5.5 %RANDOM
Rwork0.19528 ---
obs0.19837 11881 93.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.781 Å2
Baniso -1Baniso -2Baniso -3
1--3.1 Å2-1.55 Å2-0 Å2
2---3.1 Å20 Å2
3---10.07 Å2
Refinement stepCycle: 1 / Resolution: 2.7→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 8 85 2225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192167
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9732956
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565.033300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.45925.5779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99215339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4981512
X-RAY DIFFRACTIONr_chiral_restr0.1370.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211613
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5535.1841197
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.4757.7641492
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7865.388970
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.09471.7023007
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.705→2.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 42 -
Rwork0.296 921 -
obs--99.28 %

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