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- PDB-1om6: CRYSTAL STRUCTURE OF A COLD ADAPTED ALKALINE PROTEASE FROM PSEUDO... -

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Basic information

Entry
Database: PDB / ID: 1om6
TitleCRYSTAL STRUCTURE OF A COLD ADAPTED ALKALINE PROTEASE FROM PSEUDOMONAS TAC II 18, CO-CRYSTALLIZED WITH 5mM EDTA (2 MONTHS)
Componentsserralysin
KeywordsHYDROLASE / BETA JELLY ROLL
Function / homology
Function and homology information


serralysin / extracellular matrix / metalloendopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Metallo-peptidase family M12B Reprolysin-like / Peptidase M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin, C-terminal / Peptidase M10 serralysin C terminal / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. ...Metallo-peptidase family M12B Reprolysin-like / Peptidase M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin, C-terminal / Peptidase M10 serralysin C terminal / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal / Peptidase M10, metallopeptidase / Matrixin / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas sp. 'TAC II 18' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRavaud, S. / Gouet, P. / Haser, R. / Aghajari, N.
CitationJournal: J.Bacteriol. / Year: 2003
Title: Probing the role of divalent metal ions in a bacterial psychrophilic metalloprotease: binding studies of an enzyme in the crystalline state by x-ray crystallography.
Authors: Ravaud, S. / Gouet, P. / Haser, R. / Aghajari, N.
History
DepositionFeb 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: serralysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0648
Polymers48,7281
Non-polymers3377
Water6,828379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: serralysin
hetero molecules

A: serralysin
hetero molecules

A: serralysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,19224
Polymers146,1833
Non-polymers1,01021
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6110 Å2
ΔGint-130 kcal/mol
Surface area47250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)180.500, 180.500, 37.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein serralysin / CALCIUM AND ZINC DEPENDENT ALKALINE PROTEASE


Mass: 48727.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas sp. 'TAC II 18' (bacteria) / Strain: TAC II 18 / References: UniProt: O69771, serralysin
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.24 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulfate, Hepes, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Villeret, V., (1997) Protein Sci., 6, 2462.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.6 Mammonium sulfate1reservoir
20.1 MHEPES1reservoirpH7.0
315 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.5418 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 4, 2002
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.981
ReflectionResolution: 2→34.1 Å / Num. all: 30649 / Num. obs: 30649 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 13.25 Å2 / Rsym value: 0.049
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.9 % / Rsym value: 0.167 / % possible all: 100
Reflection
*PLUS
Num. measured all: 123884 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G9K

1g9k


Resolution: 2→50 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.229 1521 random
Rwork0.185 --
all0.194 --
obs0.188 30647 -
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 11 379 3720
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.62
X-RAY DIFFRACTIONc_bond_d0.0105

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