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- PDB-1smn: IDENTIFICATION OF THE SERRATIA ENDONUCLEASE DIMER: STRUCTURAL BAS... -

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Basic information

Entry
Database: PDB / ID: 1smn
TitleIDENTIFICATION OF THE SERRATIA ENDONUCLEASE DIMER: STRUCTURAL BASIS AND IMPLICATIONS FOR CATALYSIS
ComponentsEXTRACELLULAR ENDONUCLEASE
KeywordsENDONUCLEASE / NUCLEASE / DNASE / RNASE / SUGAR-NONSPECIFIC NUCLEASE
Function / homology
Function and homology information


Serratia marcescens nuclease / endonuclease activity / nucleic acid binding / extracellular region / metal ion binding
Similarity search - Function
DNA/RNA non-specific endonuclease, active site / DNA/RNA non-specific endonucleases active site. / Non-specific endonuclease / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease ...DNA/RNA non-specific endonuclease, active site / DNA/RNA non-specific endonucleases active site. / Non-specific endonuclease / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / His-Me finger superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.04 Å
AuthorsMiller, M.D. / Krause, K.L.
Citation
Journal: Protein Sci. / Year: 1996
Title: Identification of the Serratia endonuclease dimer: structural basis and implications for catalysis.
Authors: Miller, M.D. / Krause, K.L.
#1: Journal: Nat.Struct.Biol. / Year: 1994
Title: 2.1 Angstroms Structure of Serratia Endonuclease Suggests a Mechanism for Binding to Double-Stranded DNA
Authors: Miller, M.D. / Tanner, J. / Alpaugh, M. / Benedik, M.J. / Krause, K.L.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization and Preliminary Crystallographic Analysis of a Novel Nuclease from Serratia Marcescens
Authors: Miller, M.D. / Benedik, M.J. / Sullivan, M.J. / Shipley, M.C. / Krause, K.L.
History
DepositionJan 25, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: 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 / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EXTRACELLULAR ENDONUCLEASE
B: EXTRACELLULAR ENDONUCLEASE


Theoretical massNumber of molelcules
Total (without water)53,4782
Polymers53,4782
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-7 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.700, 74.500, 68.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99989, -0.014803, -0.001089), (-0.014812, 0.999846, 0.009425), (-0.000949, 0.00944, -0.999955)
Vector: -1.1809, -0.496, 103.2024)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 5 .. A 245 B 5 .. B 245 0.131

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Components

#1: Protein EXTRACELLULAR ENDONUCLEASE


Mass: 26738.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Strain: SM6 / Gene: NUCA / Plasmid: PUC19NUC4OC / Gene (production host): NUCA / Production host: Serratia marcescens (bacteria) / References: UniProt: P13717, Serratia marcescens nuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.56 Å3/Da / Density % sol: 51.93 %
Description: THIS STRUCTURE WAS SOLVED USING MULTIPLE ISOMORPHOUS REPLACEMENT WITH 5 DERIVATIVES. AFTER THE INITIAL MODEL WAS BUILT, THE DATA WAS REFINED AGAINST A NATIVE DATA SET COLLECTED FROM TWO CRYSTALS.
Crystal
*PLUS
Density % sol: 52 %
Crystal grow
*PLUS
pH: 8.2 / Method: microdialysis
Details: 2 can be substituted with 40 mM Tris-HCl, pH 8.2, 2 mM MgCl, 1 M NaCl2; or 100 mM NaPO4, pH 6.0.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11-5 mg/mlprotein11
240 mMTris-HCl12
32 mM12MgCl2
4100 mM12NaCl

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
IDWavelength
11.54
21.54
Detector
TypeIDDetectorDate
ENRAF-NONIUS FAST1DIFFRACTOMETERMar 8, 1993
ENRAF-NONIUS FAST2DIFFRACTOMETERApr 9, 1993
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection% possible obs: 93.7 % / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
MADNESdata collection
PROCORdata collection
XSCALEdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
PROCORdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.04→6 Å / σ(F): 2
Details: CRYST1 THERE IS STRONG PSEUDO-CENTERING ARISING FROM THE NON-CRYSTALLOGRAPHIC SYMMETRY. SHIFTING ONE MONOMER BY ONLY 1.4 ANGSTROMS WITH A 1 DEGREE ROTATION WOULD CHANGE THE SPACE GROUP TO I ...Details: CRYST1 THERE IS STRONG PSEUDO-CENTERING ARISING FROM THE NON-CRYSTALLOGRAPHIC SYMMETRY. SHIFTING ONE MONOMER BY ONLY 1.4 ANGSTROMS WITH A 1 DEGREE ROTATION WOULD CHANGE THE SPACE GROUP TO I 2 2 2. THIS STRUCTURE WAS SOLVED USING MULTIPLE ISOMORPHOUS REPLACEMENT WITH 5 DERIVATIVES. AFTER THE INITIAL MODEL WAS BUILT, THE DATA WAS REFINED AGAINST A NATIVE DATA SET COLLECTED FROM TWO CRYSTALS.
RfactorNum. reflection% reflection
Rwork0.168 --
obs0.168 29445 92.6 %
Displacement parametersBiso mean: 11 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 2.04→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3694 0 0 224 3918
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.81
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1
X-RAY DIFFRACTIONx_mcangle_it1.5
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6

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