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- PDB-1esp: NEUTRAL PROTEASE MUTANT E144S -

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Basic information

Entry
Database: PDB / ID: 1esp
TitleNEUTRAL PROTEASE MUTANT E144S
ComponentsNEUTRAL PROTEASE MUTANT E144S
KeywordsHYDROLASE (METALLOPROTEINASE) / INACTIVE MUTANT E144S
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: 2.8 Å
AuthorsLitster, S.A. / Wetmore, D.R. / Roche, R.S. / Codding, P.W.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: E144S active-site mutant of the Bacillus cereus thermolysin-like neutral protease at 2.8 A resolution.
Authors: Lister, S.A. / Wetmore, D.R. / Roche, R.S. / Codding, P.W.
#1: 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.
#2: 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. / Karlson, R. / Picot, D. / Jenkins, J.A. / Niklaus-Reimer, A. / Jansonius, J.N.
History
DepositionAug 11, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEUTRAL PROTEASE MUTANT E144S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0006
Polymers33,7741
Non-polymers2265
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.570, 76.570, 201.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Atom site foot note1: CIS PROLINE - PRO 52

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Components

#1: Protein NEUTRAL PROTEASE MUTANT E144S


Mass: 33774.469 Da / Num. of mol.: 1 / Mutation: E144S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria)
Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) NUMBER DSM 3101
Gene: CNP (GENBANK ACCESSION #M83910 / Plasmid: PUB18 / Gene (production host): CNP (GENBANK ACCESSION #M83910) / Production host: Bacillus subtilis (bacteria) / References: UniProt: P05806
#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.: 99 / 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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Density % sol: 51 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 %(w/v)PEG60001reservoir
250 mMpotassium succinate1reservoir
310 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceWavelength: 1.4
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 20, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4 Å / Relative weight: 1
ReflectionResolution: 2.8→55 Å / Num. obs: 8508 / % possible obs: 89 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.077
Reflection
*PLUS
Rmerge(I) obs: 0.077
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 3 Å / % possible obs: 87.5 %

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
MADNESSdata reduction
X-PLOR3phasing
RefinementResolution: 2.8→55 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.223 --
Rwork0.178 --
obs0.178 5990 89 %
Refinement stepCycle: LAST / Resolution: 2.8→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 0 5 99 2495
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.157
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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