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- PDB-1snd: STAPHYLOCOCCAL NUCLEASE DIMER CONTAINING A DELETION OF RESIDUES 1... -

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Basic information

Entry
Database: PDB / ID: 1snd
TitleSTAPHYLOCOCCAL NUCLEASE DIMER CONTAINING A DELETION OF RESIDUES 114-119 COMPLEXED WITH CALCIUM CHLORIDE AND THE COMPETITIVE INHIBITOR DEOXYTHYMIDINE-3',5'-DIPHOSPHATE
ComponentsSTAPHYLOCOCCAL NUCLEASE DIMER
KeywordsHYDROLASE / NUCLEASE / ENDONUCLEASE
Function / homology
Function and homology information


micrococcal nuclease / : / nucleic acid binding / extracellular region / metal ion binding / membrane
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.84 Å
AuthorsGreen, S.M. / Gittis, A.G. / Meeker, A.K. / Lattman, E.E.
CitationJournal: Nat.Struct.Biol. / Year: 1995
Title: One-step evolution of a dimer from a monomeric protein.
Authors: Green, S.M. / Gittis, A.G. / Meeker, A.K. / Lattman, E.E.
History
DepositionAug 23, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Dec 21, 2022Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STAPHYLOCOCCAL NUCLEASE DIMER
B: STAPHYLOCOCCAL NUCLEASE DIMER


Theoretical massNumber of molelcules
Total (without water)32,2532
Polymers32,2532
Non-polymers00
Water2,486138
1
A: STAPHYLOCOCCAL NUCLEASE DIMER
B: STAPHYLOCOCCAL NUCLEASE DIMER

A: STAPHYLOCOCCAL NUCLEASE DIMER
B: STAPHYLOCOCCAL NUCLEASE DIMER


Theoretical massNumber of molelcules
Total (without water)64,5064
Polymers64,5064
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-16 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.323, 132.323, 54.782
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

21B-337-

HOH

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Components

#1: Protein STAPHYLOCOCCAL NUCLEASE DIMER


Mass: 16126.520 Da / Num. of mol.: 2 / Mutation: DEL(114-119)
Source method: isolated from a genetically manipulated source
Details: ALTHOUGH THE LIGANDS WERE ADDED FOR CRYSTALLIZATION, THEY WERE NOT OBSERVED IN THE ELECTRON DENSITY MAPS AND WERE NOT INCLUDED IN THE FINAL STRUCTURE
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: FOGGI / Plasmid: LAMBDA PL12 / Production host: Escherichia coli (E. coli) / References: UniProt: P00644, micrococcal nuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.72 Å3/Da / Density % sol: 66.9 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.1 mMprotein1drop
21 mMPIPES1drop
350 mM1dropNaCl
510 mM1reservoirK2HPO4
640 %(w/v)MPD1reservoir
41dropCaCl2

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 34679 / % possible obs: 81 % / Observed criterion σ(I): 1 / Redundancy: 4.54 % / Rmerge(I) obs: 0.0706
Reflection
*PLUS
Highest resolution: 1.84 Å / Lowest resolution: 6 Å / Num. measured all: 157238

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
RIGAKUdata reduction
X-PLORphasing
RefinementResolution: 1.84→6 Å / Rfactor Rwork: 0.176 / σ(F): 2
Details: X-PLOR ALSO WAS USED. TOTAL NUMBER OF REFLECTIONS: 157238
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.84→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 0 138 2200
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.015
X-RAY DIFFRACTIONp_angle_d0.0310.025
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.161
X-RAY DIFFRACTIONp_mcangle_it1.9291.5
X-RAY DIFFRACTIONp_scbond_it1.5991
X-RAY DIFFRACTIONp_scangle_it2.5071.5
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1280.15
X-RAY DIFFRACTIONp_singtor_nbd0.1960.5
X-RAY DIFFRACTIONp_multtor_nbd0.2230.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1930.5
X-RAY DIFFRACTIONp_planar_tor2.93
X-RAY DIFFRACTIONp_staggered_tor2115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.120
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS

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