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- PDB-5bkm: Crystal Structure of Hip1 (Rv2224c) mutant - S228DHA (dehydroalanine) -

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Basic information

Entry
Database: PDB / ID: 5bkm
TitleCrystal Structure of Hip1 (Rv2224c) mutant - S228DHA (dehydroalanine)
ComponentsCarboxylesterase A
KeywordsHYDROLASE / serine protease
Function / homology
Function and homology information


carboxylesterase activity / cell envelope / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / post-translational protein modification / extracellular region / plasma membrane / cytosol
Similarity search - Function
: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Serine protease Hip1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 Å
AuthorsNaffin-Olivos, J.L. / Daab, A. / Goldfarb, N.E. / Doran, M.H. / Baikovitz, J. / Liu, D. / Sun, S. / White, A. / Dunn, B.M. / Rengarajan, J. ...Naffin-Olivos, J.L. / Daab, A. / Goldfarb, N.E. / Doran, M.H. / Baikovitz, J. / Liu, D. / Sun, S. / White, A. / Dunn, B.M. / Rengarajan, J. / Petsko, G.A. / Ringe, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM32415 United States
CitationJournal: To Be Published
Title: Crystal Structure of Hip1 (Rv2224c) mutant - S228DHA (dehydroalanine)
Authors: Naffin-Olivos, J.L. / Daab, A. / Goldfarb, N. / Doran, M.H. / Baikovitz, J. / Liu, D. / Sun, S. / White, A. / Dunn, B.M. / Rengarajan, J. / Petsko, G.A. / Ringe, D.
History
DepositionMar 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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: Carboxylesterase A


Theoretical massNumber of molelcules
Total (without water)52,9661
Polymers52,9661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, analytical size exclusion provided evidence Hip1 is a monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19730 Å2
Unit cell
Length a, b, c (Å)104.444, 104.444, 127.477
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 Carboxylesterase A / Hip1


Mass: 52966.176 Da / Num. of mol.: 1
Mutation: N-terminal truncation of first 49 residues and Serine228 modification to dehydroalanine
Source method: isolated from a genetically manipulated source
Details: N-terminal 6xHis Tag with linker and thrombin recognition cleavage site. Also residue serine 228 has been modified to dehydroalanine (DHA)
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: caeA, Rv2224c, MTCY427.05c / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR
References: UniProt: P9WHR3, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
Has ligand of interestY

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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: 3.79 Å3/Da / Density % sol: 67.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% (W/V) PEG3350, 0.1 M Sodium Acetate pH 5.6, 0.2 M (NH4)2SO4, 10% (V/V) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 22515 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 60.71 Å2 / Rmerge(I) obs: 0.303 / Rpim(I) all: 0.1 / Rrim(I) all: 0.314 / Χ2: 0.812 / Net I/σ(I): 2.6 / Num. measured all: 296617
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.7-2.810.622010.580.5940.51499.7
2.8-2.9111.322250.6790.4830.53199.8
2.91-3.0411.722040.8460.3650.5699.9
3.04-3.211.822270.8550.30.60899.9
3.2-3.413.722200.9420.2310.68699.90.8340.865
3.4-3.6614.522500.9680.1750.8351000.6490.672
3.66-4.0314.422490.9810.1171.0031000.4320.448
4.03-4.6214.822550.9840.0861.0241000.3230.334
4.62-5.811523060.9860.0691.0341000.2570.267
5.81-5013.823780.9910.0451.03899.60.160.166

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UNO

5uno


Resolution: 2.703→45.226 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2421 1987 8.84 %
Rwork0.1995 20497 -
obs0.2034 22484 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.12 Å2 / Biso mean: 60.6597 Å2 / Biso min: 41.74 Å2
Refinement stepCycle: final / Resolution: 2.703→45.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3500 0 0 0 3500
Num. residues----463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093586
X-RAY DIFFRACTIONf_angle_d1.1334882
X-RAY DIFFRACTIONf_chiral_restr0.043536
X-RAY DIFFRACTIONf_plane_restr0.006660
X-RAY DIFFRACTIONf_dihedral_angle_d13.7671313
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.703-2.77050.29911420.26351423100
2.7705-2.84530.32071450.26681464100
2.8453-2.92910.29331300.26531413100
2.9291-3.02360.29091410.24831453100
3.0236-3.13160.27651390.23881455100
3.1316-3.2570.29531380.23641459100
3.257-3.40520.25661400.22541431100
3.4052-3.58460.26811470.21591479100
3.5846-3.80910.24961400.18531439100
3.8091-4.1030.22071420.18241473100
4.103-4.51560.21861370.16881475100
4.5156-5.16820.20281420.16621478100
5.1682-6.50830.23691450.20241508100
6.5083-45.2260.22121590.1827154799

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