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- PDB-3h7t: Crystal structure of scabies mite inactivated protease paralogue ... -

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Basic information

Entry
Database: PDB / ID: 3h7t
TitleCrystal structure of scabies mite inactivated protease paralogue S-D1 (SMIPP-S-D1)
ComponentsGroup 3 allergen SMIPP-S YvT004A06
KeywordsHYDROLASE
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
: / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Group 3 allergen SMIPP-S YvT004A06
Similarity search - Component
Biological speciesSarcoptes scabiei type hominis (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBuckle, A.M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural mechanisms of inactivation in scabies mite serine protease paralogues.
Authors: Fischer, K. / Langendorf, C.G. / Irving, J.A. / Reynolds, S. / Willis, C. / Beckham, S. / Law, R.H. / Yang, S. / Bashtannyk-Puhalovich, T.A. / McGowan, S. / Whisstock, J.C. / Pike, R.N. / ...Authors: Fischer, K. / Langendorf, C.G. / Irving, J.A. / Reynolds, S. / Willis, C. / Beckham, S. / Law, R.H. / Yang, S. / Bashtannyk-Puhalovich, T.A. / McGowan, S. / Whisstock, J.C. / Pike, R.N. / Kemp, D.J. / Buckle, A.M.
History
DepositionApr 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Group 3 allergen SMIPP-S YvT004A06
B: Group 3 allergen SMIPP-S YvT004A06
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,30111
Polymers51,7132
Non-polymers5899
Water5,585310
1
A: Group 3 allergen SMIPP-S YvT004A06
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3809
Polymers25,8561
Non-polymers5238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Group 3 allergen SMIPP-S YvT004A06
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9222
Polymers25,8561
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.159, 133.159, 83.706
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Group 3 allergen SMIPP-S YvT004A06 / Scabies mite inactivated protease paralogue S-D1 / SMIPP-S-D1


Mass: 25856.260 Da / Num. of mol.: 2 / Fragment: UNP residues 27-261
Source method: isolated from a genetically manipulated source
Details: Expression and purification as described in Sun, J. et al. (1999) Expression and purification of recombinant human granzyme B from Pichia pastoris. Biochem Biophys Res Commun 261:251-255.
Source: (gene. exp.) Sarcoptes scabiei type hominis (arthropod)
Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / References: UniProt: Q6VPT2
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 4.14 Å3/Da / Density % sol: 70.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% v/v PEG 8000, 10% v/v Glycerol, 0.1 M Tris-HCl pH 8.5, 0.2 M Magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 7 % / Av σ(I) over netI: 3.5 / Number: 470197 / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / D res high: 1.902 Å / D res low: 115.47 Å / Num. obs: 67071 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.9857.6497.610.0440.0446.4
4.235.9810010.0450.0457.1
3.454.2310010.0560.0567.1
2.993.4510010.0710.0717.2
2.672.9910010.10.17.2
2.442.6710010.1790.1797.2
2.262.4410010.2820.2827.2
2.112.2610010.5650.5657
1.992.1110010.8660.8667.1
1.891.9996.711.4051.4056.4
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H,K,L10.579
11h,-h-k,-l20.421
ReflectionResolution: 1.89→57.64 Å / Num. obs: 67071 / % possible obs: 99.4 % / Redundancy: 7 % / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 3.495
Reflection shell

Rmerge(I) obs: 0.014 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.89-1.996.40.36139695341.40596.7
1.99-2.117.10.46535592630.866100
2.11-2.2670.56112687080.565100
2.26-2.447.22.45843681170.282100
2.44-2.677.23.55368374910.179100
2.67-2.997.274901667900.1100
2.99-3.457.28.54307759900.071100
3.45-4.237.110.93619550700.056100
4.23-5.987.114.22809739620.045100
5.98-57.646.415.31381621460.04497.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.6 Å
Translation2.5 Å38.6 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.17data scaling
PHASER1.3.2phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H7O

3h7o


Resolution: 2→57.64 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.179 / WRfactor Rwork: 0.161 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.896 / SU B: 7.104 / SU ML: 0.078 / SU R Cruickshank DPI: 0.022 / SU Rfree: 0.02 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.175 2864 5 %RANDOM
Rwork0.156 ---
obs0.157 56996 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 89.24 Å2 / Biso mean: 28.713 Å2 / Biso min: 13.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20 Å20 Å2
2--1.89 Å20 Å2
3----3.78 Å2
Refinement stepCycle: LAST / Resolution: 2→57.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 0 9 310 3847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223625
X-RAY DIFFRACTIONr_angle_refined_deg1.081.9694943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4975473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.40224.889135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38415574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.368158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212718
X-RAY DIFFRACTIONr_mcbond_it0.88922331
X-RAY DIFFRACTIONr_mcangle_it1.96253773
X-RAY DIFFRACTIONr_scbond_it3.67771294
X-RAY DIFFRACTIONr_scangle_it5.333101166
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 194 -
Rwork0.233 3985 -
all-4179 -
obs--99.95 %
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)
10.7089-0.2810.50140.6016-0.24960.6636-0.06390.02230.02230.1469-0.0305-0.0497-0.1195-0.00560.09440.150.0232-0.04510.09340.02540.0426.742877.398410.1484
21.399-0.20.69790.5477-0.31580.4796-0.10160.18420.1010.02570.0001-0.0223-0.06440.11730.10150.0892-0.0153-0.04290.17220.04310.060656.003361.958122.7603
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 235
2X-RAY DIFFRACTION2B1 - 235

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