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- PDB-1kuh: ZINC PROTEASE FROM STREPTOMYCES CAESPITOSUS -

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Basic information

Entry
Database: PDB / ID: 1kuh
TitleZINC PROTEASE FROM STREPTOMYCES CAESPITOSUS
ComponentsZINC PROTEASE
KeywordsHYDROLASE / METALLOPROTEINASE
Function / homology
Function and homology information


snapalysin / metalloendopeptidase activity / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Peptidase M7, snapalysin / Streptomyces extracellular neutral proteinase (M7) family / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Extracellular small neutral protease
Similarity search - Component
Biological speciesStreptomyces caespitosus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsKurisu, G. / Kinoshita, T. / Sugimoto, A. / Nagara, A. / Kai, Y. / Kasai, N. / Harada, S.
Citation
Journal: J.Biochem.(Tokyo) / Year: 1997
Title: Structure of the zinc endoprotease from Streptomyces caespitosus.
Authors: Kurisu, G. / Kinoshita, T. / Sugimoto, A. / Nagara, A. / Kai, Y. / Kasai, N. / Harada, S.
#1: Journal: Eur.J.Biochem. / Year: 1995
Title: Complete Amino Acid Sequence of a Zinc Metalloendoprotease from Streptomyces Caespitosus
Authors: Harada, S. / Kinoshita, T. / Kasai, N. / Tsunasawa, S. / Sakiyama, F.
#2: Journal: J.Biochem.(Tokyo) / Year: 1991
Title: Crystallization and Main-Chain Structure of Neutral Protease from Streptomyces Caespitosus
Authors: Harada, S. / Kitadokoro, K. / Kinoshita, T. / Kai, Y. / Kasai, N.
History
DepositionFeb 22, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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.ptnr1_symmetry / _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_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.ptnr3_symmetry / _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_conn.ptnr2_symmetry / _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: ZINC PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4933
Polymers14,3871
Non-polymers1052
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.210, 55.270, 37.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ZINC PROTEASE / NEUTRAL PROTEASE


Mass: 14387.327 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces caespitosus (bacteria) / References: UniProt: P56406
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 35 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Mcalcium acetate11
25-10 mg/mlprotein11
340 %(v/v)acetone11

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 19872 / Observed criterion σ(I): 2

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.6→10 Å / σ(F): 2 /
RfactorNum. reflection
Rfree0.225 -
Rwork0.164 -
obs-12279
Displacement parametersBiso mean: 10.45 Å2
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1015 0 2 93 1110
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0641.5
X-RAY DIFFRACTIONp_mcangle_it1.4942
X-RAY DIFFRACTIONp_scbond_it2.312
X-RAY DIFFRACTIONp_scangle_it3.4832.5
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.1170.12
X-RAY DIFFRACTIONp_singtor_nbd0.1510.2
X-RAY DIFFRACTIONp_multtor_nbd0.2080.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1420.2
X-RAY DIFFRACTIONp_planar_tor4.3210
X-RAY DIFFRACTIONp_staggered_tor16.24215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor23.45445
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Num. reflection obs: 12926 / Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg4.3

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