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- PDB-4nff: Human kallikrein-related peptidase 2 in complex with PPACK -

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Basic information

Entry
Database: PDB / ID: 4nff
TitleHuman kallikrein-related peptidase 2 in complex with PPACK
ComponentsKallikrein-2
KeywordsHYDROLASE / chymotrypsin-like protease / Zinc binding / extracellular
Function / homology
Function and homology information


tissue kallikrein / Activation of Matrix Metalloproteinases / secretory granule / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / serine-type endopeptidase activity / proteolysis / extracellular exosome / extracellular region
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
D-Phe-Pro-Arg-CH2Cl / Chem-0G6 / Kallikrein-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSkala, W. / Brandstetter, H. / Magdolen, V. / Goettig, P.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure-function analyses of human kallikrein-related peptidase 2 establish the 99-loop as master regulator of activity
Authors: Skala, W. / Utzschneider, D.T. / Magdolen, V. / Debela, M. / Guo, S. / Craik, C.S. / Brandstetter, H. / Goettig, P.
History
DepositionOct 31, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kallikrein-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6452
Polymers26,1911
Non-polymers4541
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.100, 60.740, 66.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kallikrein-2 / Glandular kallikrein-1 / hGK-1 / Tissue kallikrein-2


Mass: 26190.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P20151, tissue kallikrein
#2: Chemical ChemComp-0G6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / PPACK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 453.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34ClN6O3 / References: D-Phe-Pro-Arg-CH2Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.33 Å3/Da / Density % sol: 47.16 % / Mosaicity: 1.21 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 800mM ammonium sulfate, 100mM bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97004 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 19, 2011
RadiationMonochromator: Si(111); Double crystal, second crystal horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97004 Å / Relative weight: 1
ReflectionResolution: 1.9→44.94 Å / Num. all: 19421 / Num. obs: 19421 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rsym value: 0.15 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-240.6660.5851.31045126190.3060.6660.5852.392.4
2-2.124.60.520.4631.61200525850.2280.520.4633.496.5
2.12-2.275.50.4060.3692.11375324840.1650.4060.3694.797.9
2.27-2.456.40.3310.3052.51506023530.1260.3310.3056.199.2
2.45-2.6970.2690.253.11539321900.0980.2690.257.699.5
2.69-37.50.20.1864.11508720020.0710.20.18610.299.7
3-3.477.90.1250.1176.41388917600.0430.1250.1171799.8
3.47-4.2580.0790.074101213515140.0270.0790.07424.799.8
4.25-6.017.90.0580.05413.3958512120.020.0580.05426.799.8
6.01-30.377.30.0490.04616.151387020.0180.0490.04624.199

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.37 Å
Translation2.5 Å30.37 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.27 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.1948 / WRfactor Rwork: 0.1699 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8701 / SU B: 3.161 / SU ML: 0.094 / SU R Cruickshank DPI: 0.1621 / SU Rfree: 0.1447 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.146 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 988 5.1 %RANDOM
Rwork0.1973 ---
obs0.1991 19387 97.65 %-
all-19421 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.76 Å2 / Biso mean: 14.0172 Å2 / Biso min: 5.66 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 30 100 1901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021865
X-RAY DIFFRACTIONr_angle_refined_deg1.771.9682551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5615227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1923.97373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49315287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.41157
X-RAY DIFFRACTIONr_chiral_restr0.1160.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211423
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 56 -
Rwork0.252 1145 -
all-1201 -
obs--90.92 %

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