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- PDB-5euf: The crystal structure of a protease from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 5euf
TitleThe crystal structure of a protease from Helicobacter pylori
ComponentsProtease
KeywordsHYDROLASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / metal ion binding
Similarity search - Function
Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsTan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: The crystal structure of a protease from Helicobacter pylori
Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionNov 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references / Structure summary
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3938
Polymers95,9472
Non-polymers4466
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-113 kcal/mol
Surface area33380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.159, 50.266, 147.889
Angle α, β, γ (deg.)90.00, 94.86, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-609-

HOH

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Components

#1: Protein Protease /


Mass: 47973.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: pqqE, HPHPH19_0674 / Plasmid: pMCSG53 / Cell line (production host): BL21(DE3)magic / Production host: Escherichia coli (E. coli)
References: UniProt: I9VHL9, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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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: 3.02 Å3/Da / Density % sol: 59.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Calcium Acetate, 0.1M HEPES:NaOH, 10% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918, 0.97940
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
20.97941
ReflectionResolution: 2.8→48 Å / Num. all: 27514 / Num. obs: 27514 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 9
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 1.6 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→47.803 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 1191 5.08 %Random selection
Rwork0.1864 ---
obs0.1894 23449 82.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→47.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6476 0 16 29 6521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026624
X-RAY DIFFRACTIONf_angle_d0.5988981
X-RAY DIFFRACTIONf_dihedral_angle_d11.5972373
X-RAY DIFFRACTIONf_chiral_restr0.0231018
X-RAY DIFFRACTIONf_plane_restr0.0031154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.91210.3671720.25221408X-RAY DIFFRACTION47
2.9121-3.04460.3315860.251821X-RAY DIFFRACTION62
3.0446-3.20510.2981050.25322197X-RAY DIFFRACTION73
3.2051-3.40590.31221660.232499X-RAY DIFFRACTION84
3.4059-3.66870.26731890.19712789X-RAY DIFFRACTION96
3.6687-4.03780.25541540.18022894X-RAY DIFFRACTION96
4.0378-4.62160.17771250.14892923X-RAY DIFFRACTION95
4.6216-5.82110.21471470.15632872X-RAY DIFFRACTION94
5.8211-47.80980.20741470.18122855X-RAY DIFFRACTION91
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)
10.39540.3711-0.02860.88150.5590.64740.17120.4909-0.0918-0.2197-0.22010.02730.25430.59030.09760.56050.30990.08261.16980.03650.30654.323-0.208278.9429
22.95060.7182-0.00643.08661.26252.6603-0.05450.64020.2144-0.6279-0.1715-0.3376-0.51660.46740.26040.35670.1287-0.04110.44130.09160.206449.222611.025399.2512
30.66990.5004-0.87420.4556-0.50161.3896-0.04380.44570.2459-0.2491-0.0766-0.139-0.56040.4506-0.43520.4753-0.04670.04711.01250.27740.316554.965416.904888.3518
42.91521.1970.55090.49620.30741.24820.06120.57080.2682-0.0139-0.1905-0.0466-0.36520.20440.15710.3770.1294-0.02180.25240.08140.173235.118510.7303102.6147
50.37130.5172-0.01380.7309-0.16561.02910.16670.6136-0.0515-0.0256-0.1198-0.2013-0.03520.60490.04480.35330.1340.02880.78750.08220.250254.31234.351895.1045
61.77070.22450.07010.25110.58741.54460.04440.88050.1315-0.4619-0.32190.1931-0.5556-0.38840.1620.52040.2102-0.10170.5889-0.12180.256123.2216.137591.853
72.27740.1066-0.84520.88750.98662.50650.00420.4420.1469-0.2479-0.09910.0989-0.3418-0.50740.54290.48480.2055-0.10350.511-0.1430.183526.27657.711493.2422
80.36490.50670.8081.42370.50272.3829-0.06530.6947-0.2247-0.2404-0.2087-0.00360.1014-0.17540.12550.42880.08070.00830.747-0.20880.280327.5302-2.279586.1336
91.96460.01480.44020.9357-0.53972.28180.1265-0.4576-0.20750.0353-0.1667-0.06450.09940.14520.05140.1925-0.0055-0.0020.1720.12650.233849.30091.517136.9492
101.6653-0.4080.48270.6840.0641.87310.0902-0.0453-0.0522-0.053-0.207-0.06430.08310.01930.09020.2055-0.00150.02430.0235-0.00680.221438.51967.1652127.0162
111.7346-0.3851-0.33191.20310.43261.974-0.0385-0.17770.0550.2107-0.20690.01510.1088-0.32630.21250.20260.02160.00670.1725-0.09680.289322.830212.7926132.9162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 162 )
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 192 )
5X-RAY DIFFRACTION5chain 'A' and (resid 193 through 262 )
6X-RAY DIFFRACTION6chain 'A' and (resid 263 through 319 )
7X-RAY DIFFRACTION7chain 'A' and (resid 320 through 347 )
8X-RAY DIFFRACTION8chain 'A' and (resid 348 through 444 )
9X-RAY DIFFRACTION9chain 'B' and (resid 29 through 162 )
10X-RAY DIFFRACTION10chain 'B' and (resid 163 through 312 )
11X-RAY DIFFRACTION11chain 'B' and (resid 313 through 444 )

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