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- PDB-1npc: THE STRUCTURE OF NEUTRAL PROTEASE FROM BACILLUS CEREUS AT 0.2-NM ... -

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Basic information

Entry
Database: PDB / ID: 1npc
TitleTHE STRUCTURE OF NEUTRAL PROTEASE FROM BACILLUS CEREUS AT 0.2-NM RESOLUTION
ComponentsNEUTRAL PROTEASE
KeywordsHYDROLASE(METALLOPROTEINASE)
Function / homology
Function and homology information


bacillolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain ...Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsStark, W. / Pauptit, R.A. / Jansonius, J.N.
Citation
Journal: Eur.J.Biochem. / Year: 1992
Title: The structure of neutral protease from Bacillus cereus at 0.2-nm resolution.
Authors: Stark, W. / Pauptit, R.A. / Wilson, K.S. / Jansonius, J.N.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Crystal Structure of Neutral Protease from Bacillus Cereus Refined at 3.0 Angstroms Resolution and Comparison with the Homologous But More Thermostable Enzyme Thermolysin
Authors: Pauptit, R.A. / Karlsson, R. / Picot, D. / Jenkins, J.A. / Niklaus-Reimer, A. / Jansonius, J.N.
#2: Journal: Biol.Chem.Hoppe-Seyler / Year: 1986
Title: The Primary Structure of Bacillus Cereus Neutral Proteinase and Comparison with Thermolysin and Bacillus Subtilis Proteinase
Authors: Sidler, W. / Niederer, E. / Suter, F. / Zuber, H.
History
DepositionJan 8, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: 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 / pdbx_struct_special_symmetry / 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_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.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: NEUTRAL PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0426
Polymers33,8171
Non-polymers2265
Water5,477304
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.500, 76.500, 201.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Atom site foot note1: RESIDUE 52 IS A CIS PROLINE.
Components on special symmetry positions
IDModelComponents
11A-337-

HOH

21A-505-

HOH

31A-530-

HOH

41A-533-

HOH

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Components

#1: Protein NEUTRAL PROTEASE


Mass: 33816.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / References: UniProt: P05806, thermolysin
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal grow
*PLUS
Temperature: 0 K / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
218 %(w/v)PEG60001reservoir
30.05 Mpotassium succinate1reservoir
40.01 Mcalcium chloride1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 21168 / % possible obs: 88 % / Num. measured all: 195223 / Rmerge(I) obs: 0.219

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2→10 Å /
RfactorNum. reflection
obs0.175 21168
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 5 304 2699
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg2.5
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. reflection obs: 21168 / Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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