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- PDB-2bdi: Human Kallikrein 4 complex with cobalt and p-aminobenzamidine -

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Basic information

Entry
Database: PDB / ID: 2bdi
TitleHuman Kallikrein 4 complex with cobalt and p-aminobenzamidine
ComponentsKallikrein-4
KeywordsHYDROLASE / serine proteinase / s1 subsite / 70-80 loop / Structural Proteomics in Europe / SPINE / Structural Genomics
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 / secretory granule / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
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 ...: / 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
: / P-AMINO BENZAMIDINE / Kallikrein-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDebela, M. / Bode, W. / Goettig, P. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structures of human tissue kallikrein 4: activity modulation by a specific zinc binding site.
Authors: Debela, M. / Magdolen, V. / Grimminger, V. / Sommerhoff, C. / Messerschmidt, A. / Huber, R. / Friedrich, R. / Bode, W. / Goettig, P.
History
DepositionOct 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kallikrein-4
B: Kallikrein-4
C: Kallikrein-4
D: Kallikrein-4
E: Kallikrein-4
F: Kallikrein-4
G: Kallikrein-4
H: Kallikrein-4
I: Kallikrein-4
J: Kallikrein-4
K: Kallikrein-4
L: Kallikrein-4
M: Kallikrein-4
N: Kallikrein-4
O: Kallikrein-4
P: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)385,23136
Polymers382,81616
Non-polymers2,41520
Water8,215456
1
A: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1213
Polymers23,9261
Non-polymers1952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1213
Polymers23,9261
Non-polymers1952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1213
Polymers23,9261
Non-polymers1952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
M: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1213
Polymers23,9261
Non-polymers1952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
16
P: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)147.050, 73.860, 154.380
Angle α, β, γ (deg.)90.00, 102.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23926.010 Da / Num. of mol.: 16 / Fragment: Human Kallikrein 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK4, EMSP1, PRSS17, PSTS / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4]
References: UniProt: Q9Y5K2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-PBZ / P-AMINO BENZAMIDINE


Mass: 136.174 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C7H10N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 21, 2003 / Details: mirrors
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 95468 / % possible obs: 85.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.129 / Net I/σ(I): 6.99
Reflection shellResolution: 2.5→2.57 Å / % possible all: 76

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: hk4 with nickel

Resolution: 3→19.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1910575.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 3158 5 %RANDOM
Rwork0.258 ---
obs0.258 62929 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.3653 Å2 / ksol: 0.318519 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å2-2.92 Å2
2---1.78 Å20 Å2
3---3.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 3→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26720 0 164 456 27340
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.03
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_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.49
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.911.5
X-RAY DIFFRACTIONc_mcangle_it3.132
X-RAY DIFFRACTIONc_scbond_it2.632
X-RAY DIFFRACTIONc_scangle_it3.822.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.366 536 5.2 %
Rwork0.311 9779 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4PBZ.PARPBZ.TOP

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