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- PDB-1gvl: Human prokallikrein 6 (hK6)/ prozyme/ proprotease M/ proneurosin -

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Basic information

Entry
Database: PDB / ID: 1gvl
TitleHuman prokallikrein 6 (hK6)/ prozyme/ proprotease M/ proneurosin
ComponentsKALLIKREIN 6
KeywordsHYDROLASE / ZYMOGEN / HUMAN KALLIKREIN
Function / homology
Function and homology information


cornified envelope / tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / amyloid precursor protein metabolic process / hormone metabolic process / regulation of neuron projection development / protein autoprocessing / regulation of cell differentiation / collagen catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...cornified envelope / tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / amyloid precursor protein metabolic process / hormone metabolic process / regulation of neuron projection development / protein autoprocessing / regulation of cell differentiation / collagen catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / intercellular bridge / myelination / secretory granule / protein maturation / central nervous system development / response to wounding / nuclear membrane / serine-type endopeptidase activity / nucleolus / endoplasmic reticulum / mitochondrion / extracellular space / extracellular region / nucleoplasm / cytoplasm
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGomis-Ruth, F.X. / Bayes, A. / Sotiropoulou, G. / Pampalakis, G. / Tsetsenis, T. / Villegas, V. / Aviles, F.X. / Coll, M.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The Structure of Human Prokallikrein 6 Reveals a Novel Activation Mechanism for the Kallikrein Family.
Authors: Gomis-Ruth, F.X. / Bayes, A. / Sotiropoulou, G. / Pampalakis, G. / Tsetsenis, T. / Villegas, V. / Aviles, F.X. / Coll, M.
History
DepositionFeb 14, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "AB" ON SHEET RECORDS BELOW ARE ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "AB" ON SHEET RECORDS BELOW ARE ACTUALLY 7-STRANDED BARRELS. THESE ARE REPRESENTED BY 8-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KALLIKREIN 6


Theoretical massNumber of molelcules
Total (without water)24,5181
Polymers24,5181
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.000, 66.400, 71.200
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 KALLIKREIN 6 / HUMAN PROKALLIKREIN 6 / PROTEASE M / NEUROSIN / ZYME


Mass: 24517.838 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / Strain (production host): PPIC9 / References: UniProt: Q92876
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUES: ARG 19 GLN, ARG 80 GLN, ASN 134 GLN
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: 2.2 Å3/Da / Density % sol: 43 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 %PEG40001reservoir
20.1 MTris-HCl1reservoirpH8.5
30.2 M1reservoirMgCl2
410 mg/mlprotein1drop
510 mMTris-HCl1droppH8.5
610 mMbenzamidine1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.934
DetectorType: ADSC/MAR RESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→38.6 Å / Num. obs: 19445 / % possible obs: 94 % / Redundancy: 3.3 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 4.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 1.7 / % possible all: 90.1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. measured all: 64722
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 90.1 %

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Processing

Software
NameVersionClassification
CNS1refinement
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NPM

1npm


Resolution: 1.8→33.2 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: CHYMOTRYPSINOGEN A (CTGA) NUMBERING APPLIED.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1418 7 %RANDOM
Rwork0.185 ---
obs0.185 19442 94 %-
Refinement stepCycle: LAST / Resolution: 1.8→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 0 158 1874
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
% reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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