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- PDB-7sfm: Mycobacterium tuberculosis Hip1 crystal structure -

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Basic information

Entry
Database: PDB / ID: 7sfm
TitleMycobacterium tuberculosis Hip1 crystal structure
ComponentsHip1
KeywordsHYDROLASE / Mtb / AEBSF / TB / Tuberculosis / serine hydrolase
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / proteolysis
Similarity search - Function
: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
ACETATE ION / Protease
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.149 Å
AuthorsOstrov, D.A. / Li, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: 2.1 angstrom crystal structure of the Mycobacterium tuberculosis serine hydrolase, Hip1, in its anhydro-form (Anhydrohip1).
Authors: Brooks, C.L. / Ostrov, D.A. / Schumann, N.C. / Kakkad, S. / Li, D. / Pena, K. / Williams, B.P. / Goldfarb, N.E.
History
DepositionOct 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hip1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0846
Polymers51,6571
Non-polymers4275
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.891, 104.891, 127.802
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hip1 / Protease


Mass: 51656.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: tap / Production host: Escherichia coli (E. coli)
References: UniProt: A0A654TLU9, Hydrolases; Acting on peptide bonds (peptidases), Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.95 Å3/Da / Density % sol: 68.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 3350, 0.1M sodium acetate pH 5.6, 0.2 M ammonium sulfate and 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9436 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9436 Å / Relative weight: 1
ReflectionResolution: 2.149→29.464 Å / Num. obs: 44555 / % possible obs: 99 % / Redundancy: 1.1 % / Rrim(I) all: 1.72E-17 / Net I/σ(I): 17
Reflection shellResolution: 2.149→2.23 Å / Num. unique obs: 4379 / Rrim(I) all: 1.59E-17

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UGQ

5ugq


Resolution: 2.149→29.464 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2049 1996 4.48 %
Rwork0.1745 42553 -
obs0.1759 44549 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.23 Å2 / Biso mean: 24.7479 Å2 / Biso min: 10.77 Å2
Refinement stepCycle: final / Resolution: 2.149→29.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 28 466 4052
Biso mean--34.94 31.22 -
Num. residues----472
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1492-2.2030.25251420.2035298699
2.203-2.26250.25471410.1892299699
2.2625-2.3290.23611370.192300999
2.329-2.40420.23721390.1887296299
2.4042-2.49010.23471390.1787300799
2.4901-2.58970.22111430.1802301399
2.5897-2.70750.20581420.176302299
2.7075-2.85010.23621440.1796302499
2.8501-3.02850.21651440.17763021100
3.0285-3.26210.19761430.17783047100
3.2621-3.58990.17211400.16453059100
3.5899-4.10810.16561480.15383069100
4.1081-5.17130.1971430.15723116100
5.1713-29.460.19711510.193222100

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