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- PDB-6ieo: Crystal structure of Mycobacterium tuberculosis HtrA1 (Rv1223) in... -

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Basic information

Entry
Database: PDB / ID: 6ieo
TitleCrystal structure of Mycobacterium tuberculosis HtrA1 (Rv1223) in regulated conformation
ComponentsProbable serine protease HtrA (DEGP protein)
KeywordsMEMBRANE PROTEIN / Hydrolase / 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
phenylmethanesulfonic acid / Probable serine protease HtrA1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsGupta, A.K. / Gopal, B.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: The crystal structure of Mycobacterium tuberculosis high-temperature requirement A protein reveals an autoregulatory mechanism.
Authors: Gupta, A.K. / Behera, D. / Gopal, B.
History
DepositionSep 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Oct 30, 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: Probable serine protease HtrA (DEGP protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6952
Polymers32,5221
Non-polymers1721
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint4 kcal/mol
Surface area13070 Å2
Unit cell
Length a, b, c (Å)107.114, 107.114, 61.529
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-832-

HOH

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Components

#1: Protein Probable serine protease HtrA (DEGP protein) / DegQ like protein


Mass: 32522.391 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: htrA, Rv1223 / Production host: Escherichia coli (E. coli) / References: UniProt: O06291
#2: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C7H8O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M HEPES, 1.4M Sodium Citrate tribasic dihydrate pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 28, 2018 / Details: CRL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.82→37.04 Å / Num. obs: 23356 / % possible obs: 99.69 % / Redundancy: 4.6 % / Biso Wilson estimate: 29.05 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.071 / Rrim(I) all: 0.115 / Net I/σ(I): 8.5
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2197 / CC1/2: 0.517 / Rpim(I) all: 0.729 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y8T

1y8t


Resolution: 1.83→37.04 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.861 / SU ML: 0.138 / Cross valid method: FREE R-VALUE / ESU R: 0.141 / ESU R Free: 0.134 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1119 4.79 %RANDOM
Rwork0.191 ---
obs-23202 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0.39 Å20 Å2
2---0.77 Å20 Å2
3---2.5 Å2
Refinement stepCycle: 1 / Resolution: 1.83→37.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 10 138 2232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0152143
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171954
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.7432930
X-RAY DIFFRACTIONr_angle_other_deg0.4691.7184550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1215302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33821.42956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58915281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.211159
X-RAY DIFFRACTIONr_chiral_restr0.0610.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212495
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02341
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_it2.3823.261197
X-RAY DIFFRACTIONr_mcbond_other2.3813.2611198
X-RAY DIFFRACTIONr_mcangle_it3.4644.881498
X-RAY DIFFRACTIONr_mcangle_other3.4634.8811499
X-RAY DIFFRACTIONr_scbond_it2.9253.54946
X-RAY DIFFRACTIONr_scbond_other2.9243.542947
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2575.1781431
X-RAY DIFFRACTIONr_long_range_B_refined5.81242.0792218
X-RAY DIFFRACTIONr_long_range_B_other5.81142.0752219
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.825→1.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 76 -
Rwork0.326 1650 -
obs--97.85 %

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