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- PDB-1c7k: CRYSTAL STRUCTURE OF THE ZINC PROTEASE -

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Basic information

Entry
Database: PDB / ID: 1c7k
TitleCRYSTAL STRUCTURE OF THE ZINC PROTEASE
ComponentsZINC ENDOPROTEASE
KeywordsHYDROLASE / alpha and beta protein / METALLOPROTEINASE
Function / homology
Function and homology information


snapalysin / metalloendopeptidase activity / proteolysis / extracellular region / zinc ion binding
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 / AB INITIO / Resolution: 1 Å
AuthorsKurisu, G. / Harada, S. / Kai, Y.
Citation
Journal: J.Inorg.Biochem. / Year: 2000
Title: Structure of the zinc-binding site in the crystal structure of a zinc endoprotease from Streptomyces caespitosus at 1 A resolution.
Authors: Kurisu, G. / Kai, Y. / Harada, S.
#1: 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.
#2: 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.
#3: 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 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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
Revision 1.5Nov 20, 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: ZINC ENDOPROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4933
Polymers14,3871
Non-polymers1052
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.103, 55.199, 37.243
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 ENDOPROTEASE / NCNP


Mass: 14387.327 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces caespitosus (bacteria)
References: UniProt: P56406, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#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.: 116 / 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: 1 Å3/Da / Density % sol: 37.48 %
Crystal growTemperature: 277 K / Method: liquid diffusion / pH: 7
Details: acetone, pH 7.0, LIQUID DIFFUSION, temperature 277K
Crystal
*PLUS
Density % sol: 35 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method / Details: Harada, S., (1991) J.BIOCHEM.(TOKYO), 110, 46.
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

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 0.7107
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 18, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7107 Å / Relative weight: 1
ReflectionResolution: 0.92→55 Å / Num. all: 59541 / Num. obs: 59541 / % possible obs: 81.9 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.64
Reflection shellResolution: 0.92→0.97 Å / % possible all: 58.3
Reflection
*PLUS
Num. obs: 51419 / % possible obs: 82 % / Redundancy: 58.3 % / Num. measured all: 158614

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Processing

Software
NameClassification
SHELXSphasing
SHELXL-97refinement
RefinementMethod to determine structure: AB INITIO / Resolution: 1→55 Å / Num. parameters: 992 / Num. restraintsaints: 1187 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.178 344 7 %RANDOM
all0.154 4713 --
obs0.148 -75.9 %-
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1133
Refinement stepCycle: LAST / Resolution: 1→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1015 0 2 116 1133
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.09
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 51419 / Rfactor Rfree: 0.17 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.029

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