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- PDB-1g9k: CRYSTAL STRUCTURE OF A PSYCHROPHILIC ALKALINE PROTEASE FROM PSEUD... -

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Basic information

Entry
Database: PDB / ID: 1g9k
TitleCRYSTAL STRUCTURE OF A PSYCHROPHILIC ALKALINE PROTEASE FROM PSEUDOMONAS TAC II 18
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 (RNA similarity group I)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsAghajari, N. / Haser, R.
Citation
Journal: Proteins / Year: 2003
Title: Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases
Authors: Aghajari, N. / Van Petegem, F. / Villeret, V. / Chessa, J.P. / Gerday, C. / Haser, R. / Van Beeumen, J.
#1: Journal: Embo J. / Year: 1993
Title: THREE-DIMENSIONAL STRUCTURE OF THE ALKALINE PROTEASE OF PSEUDOMONAS AERUGINOSA: A TWO-DOMAIN PROTEIN WITH A CALCIUM BINDING PARALLEL BETA ROLL MOTIF
Authors: Baumann, U. / Wu, S. / Flaherty, K.M. / McKay, D.B.
History
DepositionNov 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 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_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Remark 999SEQUENCE AUTHORS CLAIM THAT THE RESIDUE 22 (33 IN SEQUENCE DATABASE) IS ASP (AND NOT GLU) AS JUDGED ...SEQUENCE AUTHORS CLAIM THAT THE RESIDUE 22 (33 IN SEQUENCE DATABASE) IS ASP (AND NOT GLU) AS JUDGED FROM ELECTRON DENSITY MAP

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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)49,17010
Polymers48,7281
Non-polymers4429
Water6,395355
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)147,50930
Polymers146,1833
Non-polymers1,32627
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 area6980 Å2
ΔGint-273 kcal/mol
Surface area50470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)186.010, 186.010, 37.970
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 (RNA similarity group I) / Genus: Pseudomonas / Strain: TAC II 18 / References: UniProt: O69771, serralysin
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / 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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulphate, Hepes, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / 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: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FU581 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 2000 / Details: mirrors
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→93.01 Å / Num. all: 34749 / Num. obs: 33263 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.1
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 2 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2029 / % possible all: 87.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A lower resolution structure (not yet deposited) solved by the molecular replacement method using pdb entry 1KAP as a search model

1kap


Resolution: 1.96→46.13 Å
Isotropic thermal model: overall anisotropic B-factor correction algorithm from CNS
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.187 3304 -random
Rwork0.156 ---
all-35179 --
obs-33261 94.5 %-
Displacement parametersBiso mean: 18.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.96→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3387 0 13 355 3755
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.179
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.65
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.159
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.65

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