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- PDB-1smp: CRYSTAL STRUCTURE OF A COMPLEX BETWEEN SERRATIA MARCESCENS METALL... -

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Basic information

Entry
Database: PDB / ID: 1smp
TitleCRYSTAL STRUCTURE OF A COMPLEX BETWEEN SERRATIA MARCESCENS METALLO-PROTEASE AND AN INHIBITOR FROM ERWINIA CHRYSANTHEMI
Components
  • ERWINIA CHRYSANTHEMI INHIBITOR
  • SERRATIA METALLO PROTEINASE
KeywordsCOMPLEX (METALLOPROTEASE/INHIBITOR) / COMPLEX (METALLOPROTEASE-INHIBITOR) / COMPLEX (METALLOPROTEASE-INHIBITOR) complex
Function / homology
Function and homology information


serralysin / metalloendopeptidase inhibitor activity / symbiont-mediated killing of host cell / extracellular matrix / metalloendopeptidase activity / toxin activity / periplasmic space / calcium ion binding / proteolysis / extracellular space ...serralysin / metalloendopeptidase inhibitor activity / symbiont-mediated killing of host cell / extracellular matrix / metalloendopeptidase activity / toxin activity / periplasmic space / calcium ion binding / proteolysis / extracellular space / extracellular region / zinc ion binding
Similarity search - Function
Protease inhibitor / Alkaline proteinase inhibitor/ Outer membrane lipoprotein Omp19 / Protease inhibitor Inh / Protease inhibitor, beta-barrel domain / Lipocalin - #10 / Peptidase M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin, C-terminal / Peptidase M10 serralysin C terminal / Serralysin-like metalloprotease, C-terminal ...Protease inhibitor / Alkaline proteinase inhibitor/ Outer membrane lipoprotein Omp19 / Protease inhibitor Inh / Protease inhibitor, beta-barrel domain / Lipocalin - #10 / 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 / Lipocalin / Neutral zinc metallopeptidases, zinc-binding region signature. / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Proteinase inhibitor / Serralysin
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
Erwinia chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsBaumann, U. / Bauer, M. / Letoffe, S. / Delepelaire, P. / Wandersman, C.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of a complex between Serratia marcescens metallo-protease and an inhibitor from Erwinia chrysanthemi.
Authors: Baumann, U. / Bauer, M. / Letoffe, S. / Delepelaire, P. / Wandersman, C.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystal Structure of the 50 kDa Metallo-Proteinase from Serratia Marcescens
Authors: Baumann, U.
History
DepositionJan 13, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_asym_id / _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.ptnr3_auth_asym_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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERRATIA METALLO PROTEINASE
I: ERWINIA CHRYSANTHEMI INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,80610
Polymers61,4602
Non-polymers3468
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-71 kcal/mol
Surface area22220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.830, 108.830, 87.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein SERRATIA METALLO PROTEINASE


Mass: 50439.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: INH / Plasmid: PUC / Gene (production host): INH / Production host: Escherichia coli (E. coli) / References: UniProt: P23694, serralysin
#2: Protein ERWINIA CHRYSANTHEMI INHIBITOR


Mass: 11020.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Gene: INH / Plasmid: PUC / Gene (production host): INH / Production host: Escherichia coli (E. coli) / References: UniProt: P18958
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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

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Sample preparation

CrystalDensity Matthews: 4.24 Å3/Da / Density % sol: 70.96 %
Crystal
*PLUS
Density % sol: 70 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 9 / PH range high: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.1-1.3 Mammonium sulfate1drop
20.9-1.4 Mphosphate1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS X1000 / Detector: AREA DETECTOR / Date: Mar 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 40845 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.057
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 54249 / Num. measured all: 192406 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.35 Å / % possible obs: 76 % / Rmerge(I) obs: 0.211

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Processing

Software
NameClassification
XDSdata scaling
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 2.3→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.247 -
Rwork0.195 -
obs0.195 40347
Displacement parametersBiso mean: 30.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4307 0 8 221 4536
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.49
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.52
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.192
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.52
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.192

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