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- PDB-6nvb: Crystal structure of the inhibitor-free form of the serine protea... -

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Basic information

Entry
Database: PDB / ID: 6nvb
TitleCrystal structure of the inhibitor-free form of the serine protease kallikrein-4
ComponentsKallikrein-4
KeywordsHYDROLASE / protease / klk4
Function / homology
Function and homology information


biomineral tissue development / amelogenesis / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / serine-type peptidase activity / protein maturation / secretory granule / serine-type endopeptidase activity / proteolysis / extracellular space ...biomineral tissue development / amelogenesis / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / serine-type peptidase activity / protein maturation / secretory granule / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
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: 1.636 Å
AuthorsRiley, B.T. / Buckle, A.M. / McGowan, S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structure of the inhibitor-free form of the serine protease kallikrein-4.
Authors: Riley, B.T. / Hoke, D.E. / McGowan, S. / Buckle, A.M.
History
DepositionFeb 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 28, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Oct 11, 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 1.4Nov 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: Kallikrein-4
B: Kallikrein-4
C: Kallikrein-4
D: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,79712
Polymers96,0524
Non-polymers7458
Water19,3481074
1
A: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1052
Polymers24,0131
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2934
Polymers24,0131
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1052
Polymers24,0131
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2934
Polymers24,0131
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.602, 65.723, 74.191
Angle α, β, γ (deg.)79.010, 72.910, 77.620
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Kallikrein-4 / Enamel matrix serine proteinase 1 / Kallikrein-like protein 1 / KLK-L1 / Prostase / Serine protease 17


Mass: 24013.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK4, EMSP1, PRSS17, PSTS / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y5K2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1074 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2M lithium sulfate, 0.1M sodium acetate, 22% PEG 8000 cryoprotectant = 1:1 glycerol : mother liquor

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid N2 vapor stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 5, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.636→35.8 Å / Num. obs: 107669 / % possible obs: 96.78 % / Redundancy: 3.9 % / Biso Wilson estimate: 15.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06342 / Rpim(I) all: 0.03715 / Rrim(I) all: 0.07355 / Net I/av σ(I): 17.81 / Net I/σ(I): 17.81
Reflection shellResolution: 1.636→1.695 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.6866 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 10360 / CC1/2: 0.698 / Rpim(I) all: 0.4039 / Rrim(I) all: 0.7973 / % possible all: 93.42

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSNov 1, 2016data reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
Coot0.8.9.1model building
PHENIX1.14.3260refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K8Y

4k8y


Resolution: 1.636→35.8 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.1803 5369 -Random
Rwork0.1541 ---
obs-107659 96.78 %-
Displacement parametersBiso mean: 21.54 Å2
Refinement stepCycle: LAST / Resolution: 1.636→35.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6690 0 46 1074 7810
LS refinement shellResolution: 1.636→1.695 Å
RfactorNum. reflection% reflection
Rfree0.27 485 -
Rwork0.2494 10360 -
obs--93.42 %

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