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- PDB-3bsq: Crystal structure of human kallikrein 7 produced as a secretion p... -

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Basic information

Entry
Database: PDB / ID: 3bsq
TitleCrystal structure of human kallikrein 7 produced as a secretion protein in E.coli
ComponentsKallikrein-7
KeywordsHYDROLASE / serine proteases / kallikreins / LD6 / X-ray crystal structure / Glycoprotein / Secreted / Zymogen
Function / homology
Function and homology information


stratum corneum chymotryptic enzyme / positive regulation of antibacterial peptide production / epidermal lamellar body / cornified envelope / extracellular matrix disassembly / epidermis development / serine-type peptidase activity / Degradation of the extracellular matrix / secretory granule / metalloendopeptidase activity ...stratum corneum chymotryptic enzyme / positive regulation of antibacterial peptide production / epidermal lamellar body / cornified envelope / extracellular matrix disassembly / epidermis development / serine-type peptidase activity / Degradation of the extracellular matrix / secretory granule / metalloendopeptidase activity / peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / 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 domain profile. / Serine proteases, trypsin family, serine active site. / 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 domain profile. / Serine proteases, trypsin family, serine active site. / 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 / molecular replacement / Resolution: 2.8 Å
AuthorsFernandez, I.S. / Standker, L. / Magert, H.J. / Forssmann, W.G. / Gimenez-Gallego, G. / Romero, A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of human epidermal kallikrein 7 (hK7) synthesized directly in its native state in E. coli: insights into the atomic basis of its inhibition by LEKTI domain 6 (LD6)
Authors: Fernandez, I.S. / Standker, L. / Magert, H.J. / Forssmann, W.G. / Gimenez-Gallego, G. / Romero, A.
History
DepositionDec 26, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Kallikrein-7
B: Kallikrein-7
C: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,19419
Polymers74,6573
Non-polymers1,53716
Water54030
1
A: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4627
Polymers24,8861
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4627
Polymers24,8861
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2705
Polymers24,8861
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.580, 113.580, 326.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Kallikrein-7 / / hK7 / Stratum corneum chymotryptic enzyme / hSCCE / Serine protease 6


Mass: 24885.520 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK7 / Plasmid: pRHO / Production host: Escherichia coli (E. coli)
References: UniProt: P49862, stratum corneum chymotryptic enzyme
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.2M AMMONIUM SULFATE, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93
DetectorType: ADSC QUANTUM 1 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.8→54.39 Å / Num. all: 19430 / Num. obs: 19524 / % possible obs: 99 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 9.4
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2816 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NPM

1npm


Resolution: 2.8→50 Å / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: TLS refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.2915 1027 -RANDOM
Rwork0.2169 ---
all-20076 --
obs-19424 98.33 %-
Displacement parametersBiso mean: 37.111 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5038 0 80 30 5148
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_angle_refined_deg1.154
LS refinement shellHighest resolution: 2.8 Å
RfactorNum. reflection% reflection
Rfree0.2915 1027 -
Rwork0.2169 --
obs-20076 98.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4184-0.53660.17160.2889-0.030.2835-0.0214-0.0020.0315-0.0282-0.0163-0.02380.0778-0.02870.0330.17970.02910.00310.17320.00030.2011-41.235416.210829.4164
20.2702-0.07440.06160.3922-0.21380.44280.04880.0330.0392-0.07680.0202-0.05890.1571-0.1624-0.06680.22230.0047-0.01690.2204-0.01870.1866-22.5129-7.093943.5743
30.23560.1391-0.35740.5056-0.4110.3340.0211-0.0309-0.062-0.0716-0.0595-0.11190.08610.00630.03270.21280.02-0.02950.2457-0.00820.2064-29.4562-15.19117.019
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA16 - 2381 - 223
2X-RAY DIFFRACTION2BB16 - 2371 - 222
3X-RAY DIFFRACTION3CC16 - 2381 - 223

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