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- PDB-3ujz: Crystal structure of enterohemorrhagic E. coli StcE -

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Basic information

Entry
Database: PDB / ID: 3ujz
TitleCrystal structure of enterohemorrhagic E. coli StcE
ComponentsMetalloprotease stcE
KeywordsHYDROLASE / metalloprotease / mucin-type glycoprotein
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Gamma-B Crystallin; domain 1 - #40 / Peptidase M66 domain / ToxR activated gene A lipoprotein domain / : / Peptidase M66 / ToxR activated gene A lipoprotein domain / Metalloprotease StcE, beta-sandwich domain / Peptidase family M66 domain profile. / Metalloprotease StcE, C-terminal / Beta/Gamma crystallin ...Gamma-B Crystallin; domain 1 - #40 / Peptidase M66 domain / ToxR activated gene A lipoprotein domain / : / Peptidase M66 / ToxR activated gene A lipoprotein domain / Metalloprotease StcE, beta-sandwich domain / Peptidase family M66 domain profile. / Metalloprotease StcE, C-terminal / Beta/Gamma crystallin / Gamma-B Crystallin; domain 1 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Metalloprotease StcE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsYu, A.C.Y. / Strynadka, N.C.J.
CitationJournal: Structure / Year: 2012
Title: Structural Insight into the Bacterial Mucinase StcE Essential to Adhesion and Immune Evasion during Enterohemorrhagic E. coli Infection.
Authors: Yu, A.C. / Worrall, L.J. / Strynadka, N.C.
History
DepositionNov 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metalloprotease stcE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9622
Polymers96,8971
Non-polymers651
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Metalloprotease stcE
hetero molecules

A: Metalloprotease stcE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,9254
Polymers193,7942
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1320 Å2
ΔGint-79 kcal/mol
Surface area49560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.530, 186.000, 188.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Metalloprotease stcE / Mucinase / Neutral zinc metalloprotease stcE / Secreted protease of C1 esterase inhibitor from EHEC


Mass: 96897.070 Da / Num. of mol.: 1 / Mutation: K318A, K320A, E321A, E447D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: stcE, tagA, L7031, ECO57PM83 / Production host: Escherichia coli (E. coli)
References: UniProt: O82882, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 3.47 Å3/Da / Density % sol: 64.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M MgCl2, 8% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97907 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 27, 2011
RadiationMonochromator: DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.5→66.27 Å / Num. all: 47052 / Num. obs: 47011 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.8 % / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→48.17 Å / Cor.coef. Fo:Fc: 0.9162 / Cor.coef. Fo:Fc free: 0.8815 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 2349 5 %RANDOM
Rwork0.2114 ---
obs0.2134 47011 --
all-47052 --
Displacement parametersBiso mean: 84.6 Å2
Baniso -1Baniso -2Baniso -3
1-12.1612 Å20 Å20 Å2
2---24.3314 Å20 Å2
3---12.1702 Å2
Refine analyzeLuzzati coordinate error obs: 0.534 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4695 0 1 172 4868
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014815HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.26544HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1602SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes127HARMONIC2
X-RAY DIFFRACTIONt_gen_planes702HARMONIC5
X-RAY DIFFRACTIONt_it4815HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion21.22
X-RAY DIFFRACTIONt_chiral_improper_torsion608SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5400SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2539 180 5.24 %
Rwork0.2309 3253 -
all0.2321 3433 -
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)
17.0061-0.8731-0.78942.324-0.12924.885-0.06620.22620.21620.08130.16640.354-0.1815-0.9577-0.1001-0.02360.05130.04690.977-0.07770.1398-29.54141.48763.333
24.2932-0.5706-0.98850.66530.44343.450.0211-0.35510.85810.04790.12410.0318-0.3878-0.5546-0.14520.06650.03320.08920.7848-0.18490.3042-20.91545.00668.34
34.6083-0.6249-0.48150.97270.23773.3901-0.0202-0.7034-0.08920.19340.163-0.21640.45110.8845-0.14270.08340.2038-0.01251.0343-0.17220.09149.19631.41872.098
45.4773-1.0623-0.97041.0430.73033.31410.16710.18350.6791-0.05120.0403-0.1177-0.23590.2007-0.20740.0244-0.03850.08940.7023-0.06770.153-3.85342.27257.471
534.1844-42.191420.620326.7089-18.678729.3223-1.0292.08451.72410.20471.7477-0.9331-0.5431-0.6311-0.71870.21480.51010.1748-0.8567-0.50320.8171-6.2942.08353.173
62.983-0.3218-0.77381.4897-0.44793.9835-0.1146-0.6589-0.28660.38560.18030.08110.81280.0319-0.06560.29660.0390.06320.8576-0.03750.2241-9.56327.26772.492
73.28960.0334-1.26511.78831.14772.60770.1319-0.9912-0.39410.4871-0.0261-0.37010.8970.8547-0.10580.37630.3967-0.11221.5082-0.01040.126811.06726.65484.419
86.203-0.28871.11961.91320.8186.13360.052-0.56040.16970.1346-0.23350.05470.55430.05020.18150.139-0.06970.11871.1243-0.16610.0908-21.32339.91797.283
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|39 - A|115 }A39 - 115
2X-RAY DIFFRACTION2{ A|116 - A|310 }A116 - 310
3X-RAY DIFFRACTION3{ A|311 - A|411 }A311 - 411
4X-RAY DIFFRACTION4{ A|412 - A|512 }A412 - 512
5X-RAY DIFFRACTION5{ A|513 - A|519 }A513 - 519
6X-RAY DIFFRACTION6{ A|520 - A|685 }A520 - 685
7X-RAY DIFFRACTION7{ A|686 - A|800 }A686 - 800
8X-RAY DIFFRACTION8{ A|801 - A|898 }A801 - 898

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