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- PDB-1mzd: crystal structure of human pro-granzyme K -

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Basic information

Entry
Database: PDB / ID: 1mzd
Titlecrystal structure of human pro-granzyme K
Componentspro-granzyme K
KeywordsHYDROLASE / granzyme / apoptosis / serine protease / S1 family
Function / homology
Function and homology information


granzyme-mediated programmed cell death signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / protein maturation / serine-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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 / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsHink-Schauer, C. / Estebanez-Perpina, E. / Wilharm, E. / Fuentes-Prior, P. / Klinkert, W. / Bode, W. / Jenne, D.E.
CitationJournal: J.BIOL.CHEM. / Year: 2002
Title: The 2.2-A Crystal Structure of Human Pro-granzyme K Reveals a Rigid Zymogen with Unusual Features
Authors: Hink-Schauer, C. / Estebanez-Perpina, E. / Wilharm, E. / Fuentes-Prior, P. / Klinkert, W. / Bode, W. / Jenne, D.E.
History
DepositionOct 7, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 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 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 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: pro-granzyme K


Theoretical massNumber of molelcules
Total (without water)26,1341
Polymers26,1341
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.750, 78.860, 85.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein pro-granzyme K / granzyme K / granzyme 3 / NK-tryptase-2


Mass: 26134.189 Da / Num. of mol.: 1 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: bone marrow / Plasmid: pET24c+ / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3)
References: UniProt: P49863, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.04 Å3/Da / Density % sol: 39.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 1.6M sodium formate, 2.5mM 2-[N-morpholino]ethane-sulfonic acid, 50mM sodium chloride, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
23.2 Msodium formate1reservoirpH8.4

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 26, 2000
RadiationMonochromator: CuK alpha / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 39313 / Num. obs: 10537 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.147
Reflection shellResolution: 2.9→3 Å / Num. unique all: 477 / % possible all: 92.5
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 50 Å / % possible obs: 94.5 % / Num. measured all: 39313
Reflection shell
*PLUS
% possible obs: 92.5 %

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Processing

Software
NameClassification
MOSFLMdata reduction
CCP4data reduction
AMoREphasing
CNSrefinement
CCP4data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: granzyme B

Resolution: 2.9→22 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.316738 498 -random
Rwork0.223642 ---
all-4549 --
obs-498 88.8 %-
Displacement parametersBiso mean: 26.8 Å2
Refinement stepCycle: LAST / Resolution: 2.9→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1829 0 0 30 1859
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.28094
X-RAY DIFFRACTIONc_bond_d0.006722
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 22 Å / Num. reflection obs: 9771 / Num. reflection Rfree: 500 / Rfactor Rfree: 0.3167 / Rfactor Rwork: 0.2236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.28

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