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- PDB-8e5w: Crystal structure of dehydroalanine Hip1 -

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Basic information

Entry
Database: PDB / ID: 8e5w
TitleCrystal structure of dehydroalanine Hip1
ComponentsProtease
KeywordsHYDROLASE / serine protease Hip1
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
DI(HYDROXYETHYL)ETHER / PALMITIC ACID / Protease
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGoldfarb, N.E. / Brooks, C.L. / Ostrov, D.A.
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
DepositionAug 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7825
Polymers52,2171
Non-polymers5654
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
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
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Protease


Mass: 52217.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: tap, ERS007688_01841 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A654TLU9, Hydrolases; Acting on peptide bonds (peptidases), Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O
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: 3.89 Å3/Da / Density % sol: 68.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: ammonium sulfate PEG 8000 sodium cacodylate trihydrate pH 6.5

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9436 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 44570 / % possible obs: 99.5 % / Redundancy: 6.1 % / Biso Wilson estimate: 22.99 Å2 / Rmerge(I) obs: 0.116 / Χ2: 1.523 / Net I/σ(I): 7.7 / Num. measured all: 270167
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.15-2.195.40.56421811.439198.9
2.19-2.236.10.51521941.467199.1
2.23-2.276.10.46522021.469199.1
2.27-2.326.10.42921761.504199
2.32-2.376.10.38921981.495199.1
2.37-2.426.10.35721771.509199.3
2.42-2.486.10.31222171.518199.5
2.48-2.556.10.28122161.533199.5
2.55-2.626.10.26222061.543199.2
2.62-2.716.10.21822071.608199.5
2.71-2.816.10.18521951.553199.4
2.81-2.926.10.16122391.629199.5
2.92-3.056.10.13422141.615199.6
3.05-3.216.10.10722281.579199.7
3.21-3.416.10.08522451.569199.8
3.41-3.676.10.06822391.533199.8
3.67-4.046.10.05722721.56199.9
4.04-4.636.10.0522591.517199.9
4.63-5.8260.0523021.4191100
5.82-105.70.04324031.386199.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UNO

5uno


Resolution: 2.15→29.46 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1896 2248 5.05 %
Rwork0.16 42297 -
obs0.1615 44545 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.73 Å2 / Biso mean: 30.0853 Å2 / Biso min: 12.95 Å2
Refinement stepCycle: final / Resolution: 2.15→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3530 0 88 542 4160
Biso mean--45.44 35.02 -
Num. residues----470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.20.23191520.18822574272699
2.2-2.250.20341390.17922596273599
2.25-2.30.21051470.17092587273499
2.3-2.370.19521330.16152624275799
2.37-2.430.20291500.16342603275399
2.44-2.510.20251410.16062583272499
2.51-2.60.19591280.157626272755100
2.6-2.710.19921290.1572661279099
2.71-2.830.17931350.160426342769100
2.83-2.980.1941580.163226022760100
2.98-3.170.19411320.15626612793100
3.17-3.410.19291450.159426522797100
3.41-3.750.1831430.142226622805100
3.75-4.290.15111210.136826992820100
4.3-5.40.17341530.147627042857100
5.41-29.460.20421420.200428282970100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.75820.11420.32321.99270.47473.2403-0.07730.14640.3225-0.23280.07620.24680.0097-0.25750.00720.1995-0.0643-0.0570.17730.06440.276920.4117-27.7591-10.6093
21.30740.82620.34780.81430.0380.43320.0042-0.11180.11670.0381-0.02020.16010.0253-0.12710.01780.1862-0.012-0.00380.1847-0.01590.188331.7953-29.50532.9819
36.64032.5546-5.76630.9273-2.31444.9343-0.0099-0.1267-0.11370.0201-0.04870.00940.25980.10230.09560.25050.0026-0.00130.15260.02220.188551.0228-40.715-4.4345
41.2663-0.1124-0.2852.93671.872.1376-0.04110.05240.0765-0.0180.0614-0.2067-0.03810.2881-0.00290.1631-0.02080.01420.15750.04690.145361.8098-25.8421-5.0385
51.61160.063-0.86680.63010.111.8025-0.0010.04980.0963-0.1134-0.06180.0555-0.023-0.02820.06140.1724-0.0143-0.03140.12820.00190.14746.6421-25.9881-5.8092
61.0958-0.2795-0.85243.66640.71085.7259-0.088-0.1113-0.21190.1952-0.0202-0.08520.55370.06220.13470.1961-0.0172-0.01160.12910.03930.158754.0258-35.873110.4532
71.29720.20180.18670.9842-0.06780.93910.01860.0391-0.1732-0.12520.02790.01530.2314-0.0971-0.03790.2269-0.0523-0.00440.15040.00160.185832.4777-44.9674-6.644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 149 )A44 - 149
2X-RAY DIFFRACTION2chain 'A' and (resid 150 through 259 )A150 - 259
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 284 )A260 - 284
4X-RAY DIFFRACTION4chain 'A' and (resid 285 through 329 )A285 - 329
5X-RAY DIFFRACTION5chain 'A' and (resid 330 through 401 )A330 - 401
6X-RAY DIFFRACTION6chain 'A' and (resid 402 through 431 )A402 - 431
7X-RAY DIFFRACTION7chain 'A' and (resid 432 through 520 )A432 - 520

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