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- PDB-3tk9: Crystal structure of human granzyme H -

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Basic information

Entry
Database: PDB / ID: 3tk9
TitleCrystal structure of human granzyme H
ComponentsGranzyme H
KeywordsHYDROLASE / serine protease / Cytolysis
Function / homology
Function and homology information


cytolytic granule / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Metabolism of Angiotensinogen to Angiotensins / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / killing of cells of another organism / intracellular membrane-bounded organelle / serine-type endopeptidase activity / apoptotic process / proteolysis / membrane / cytoplasm
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, L. / Zhang, K. / Wu, L. / Tong, L. / Sun, F. / Fan, Z.
CitationJournal: J.Immunol. / Year: 2012
Title: Structural insights into the substrate specificity of human granzyme H: the functional roles of a novel RKR motif
Authors: Wang, L. / Zhang, K. / Wu, L. / Liu, S. / Zhang, H. / Zhou, Q. / Tong, L. / Sun, F. / Fan, Z.
History
DepositionAug 25, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 1, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Granzyme H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3072
Polymers25,2111
Non-polymers961
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.885, 63.885, 142.464
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Granzyme H / GzmH / CCP-X / Cathepsin G-like 2 / CTSGL2 / Cytotoxic T-lymphocyte proteinase / Cytotoxic serine ...GzmH / CCP-X / Cathepsin G-like 2 / CTSGL2 / Cytotoxic T-lymphocyte proteinase / Cytotoxic serine protease C / CSP-C


Mass: 25211.432 Da / Num. of mol.: 1 / Mutation: D103N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GZMH, CGL2, CTSGL2 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta(DE3)
References: UniProt: P20718, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.88 Å3/Da / Density % sol: 57.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Li2SO4, 0.1M Bicine (pH 8.5), 25% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 28, 2008
RadiationMonochromator: Triangular Si(111) with an asymmetric angle of 7.8
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 15662 / Num. obs: 15537 / % possible obs: 99.2 % / Observed criterion σ(I): -0.5 / Redundancy: 8.8 % / Biso Wilson estimate: 35.2 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 31.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1486 / % possible all: 98.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IAU

1iau


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.771 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27657 776 5 %RANDOM
Rwork0.25104 ---
all0.279 15662 --
obs0.25223 14758 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.541 Å2
Baniso -1Baniso -2Baniso -3
1-2.84 Å20 Å20 Å2
2--2.84 Å20 Å2
3----5.69 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 5 41 1815
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.015
X-RAY DIFFRACTIONr_angle_refined_deg1.761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.817
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.708
X-RAY DIFFRACTIONr_chiral_restr0.122
X-RAY DIFFRACTIONr_gen_planes_refined0.007
X-RAY DIFFRACTIONr_mcbond_it0.79
X-RAY DIFFRACTIONr_mcangle_it1.445
X-RAY DIFFRACTIONr_scbond_it2.061
X-RAY DIFFRACTIONr_scangle_it3.345
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 54 -
Rwork0.371 1009 -
obs--96.29 %

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