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- PDB-3g01: Structure of GrC mutant E192R/E193G -

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Basic information

Entry
Database: PDB / ID: 3g01
TitleStructure of GrC mutant E192R/E193G
ComponentsGranzyme C
KeywordsHYDROLASE / Cytolysis / Protease / Serine protease / Zymogen
Function / homology
Function and homology information


cytolytic granule / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / killing of cells of another organism / serine-type endopeptidase activity / intracellular membrane-bounded organelle / proteolysis / cytoplasm
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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 ...Serine proteases, trypsin family, histidine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBuckle, A.M. / Kaiserman, D. / Whisstock, J.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of granzyme C reveals an unusual mechanism of protease autoinhibition
Authors: Kaiserman, D. / Buckle, A.M. / Van Damme, P. / Irving, J.A. / Law, R.H.P. / Matthews, A.Y. / Bashtannyk-Puhalovich, T. / Langendorf, C. / Thompson, P. / Vandekerckhove, J. / Gevaert, K. / ...Authors: Kaiserman, D. / Buckle, A.M. / Van Damme, P. / Irving, J.A. / Law, R.H.P. / Matthews, A.Y. / Bashtannyk-Puhalovich, T. / Langendorf, C. / Thompson, P. / Vandekerckhove, J. / Gevaert, K. / Whisstock, J.C. / Bird, P.I.
History
DepositionJan 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Granzyme C
B: Granzyme C


Theoretical massNumber of molelcules
Total (without water)50,2962
Polymers50,2962
Non-polymers00
Water50428
1
A: Granzyme C


Theoretical massNumber of molelcules
Total (without water)25,1481
Polymers25,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Granzyme C


Theoretical massNumber of molelcules
Total (without water)25,1481
Polymers25,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.375, 71.375, 207.171
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEGLNGLNAA21 - 2221 - 202
21ILEILEGLNGLNBB21 - 2221 - 202
12GLYGLYHISHISAA225 - 247205 - 227
22GLYGLYHISHISBB225 - 247205 - 227

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Components

#1: Protein Granzyme C / Cytotoxic cell protease 2 / CCP2 / B10


Mass: 25148.055 Da / Num. of mol.: 2 / Fragment: UNP residues 21-247 / Mutation: E201R, E202G
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.) Mus musculus (house mouse) / Production host: Pichia pastoris (fungus)
References: UniProt: P08882, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN IS BASED ON REFERENCE 3 OF UNIPROTKB/SWISS-PROT P08882 (GRAC_MOUSE).

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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: 3.03 Å3/Da / Density % sol: 59.39 % / Mosaicity: 0.37 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.2M ammonium sulfate, 0.25g/ml PEG 3350, 0.1M sodium cacodylate, pH 6.6, 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: May 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 4.6 % / Av σ(I) over netI: 9.4 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / D res high: 2.496 Å / D res low: 61.812 Å / Num. obs: 20089 / % possible obs: 97.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.9161.8193.810.0320.0324.5
5.597.919610.0370.0374.6
4.565.5996.510.0360.0364.6
3.954.5697.210.0380.0384.6
3.543.9597.210.050.054.6
3.233.5497.410.0860.0864.6
2.993.2397.810.1540.1544.6
2.82.9998.210.2790.2794.6
2.642.898.410.4680.4684.5
2.52.6498.610.7160.7164.5
ReflectionResolution: 2.496→61.812 Å / Num. obs: 20089 / % possible obs: 97.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 9.362
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.644.50.7161.11343329740.71698.6
2.64-2.84.50.4681.61256127700.46898.4
2.8-2.994.60.2792.71201226380.27998.2
2.99-3.234.60.1544.81105424290.15497.8
3.23-3.544.60.0868.41020322250.08697.4
3.54-3.954.60.0513.4927520180.0597.2
3.95-4.564.60.03816811217660.03897.2
4.56-5.594.60.03617.5693214960.03696.5
5.59-7.914.60.03715.9532111540.03796
7.91-61.814.50.03217.927776190.03293.8

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.17data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A1U

1a1u


Resolution: 2.5→59.23 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.223 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.833 / SU B: 18.739 / SU ML: 0.185 / SU R Cruickshank DPI: 0.379 / SU Rfree: 0.245 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.367 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.236 992 4.9 %RANDOM
Rwork0.212 ---
obs0.213 20087 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 69.77 Å2 / Biso mean: 33.373 Å2 / Biso min: 11.25 Å2
Baniso -1Baniso -2Baniso -3
1-3.68 Å21.84 Å20 Å2
2--3.68 Å20 Å2
3----5.52 Å2
Refinement stepCycle: LAST / Resolution: 2.5→59.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 0 28 3082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213125
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9434257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0065413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.60623.5120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1915442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3651516
X-RAY DIFFRACTIONr_chiral_restr0.090.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212378
X-RAY DIFFRACTIONr_mcbond_it1.532075
X-RAY DIFFRACTIONr_mcangle_it2.80553293
X-RAY DIFFRACTIONr_scbond_it3.95271050
X-RAY DIFFRACTIONr_scangle_it5.63510964
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1522 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.020.05
TIGHT THERMAL0.050.5
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 66 -
Rwork0.303 1425 -
all-1491 -
obs--97.77 %
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)
11.0205-0.3870.06281.856-0.59075.7428-0.10030.0367-0.03610.04890.0978-0.0132-0.3419-0.05470.00250.10940.0454-0.01640.12090.0770.175427.18-41.403-6.519
21.224-0.54810.50051.6946-0.34615.6910.0861-0.03240.0381-0.0634-0.09540.02570.20540.24460.00930.1620.0162-0.06330.07110.05160.175613.42-17.576-27.931
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 247
2X-RAY DIFFRACTION2B21 - 247

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