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- PDB-2enb: CRYSTAL STRUCTURES OF THE BINARY CA2+ AND PDTP COMPLEXES AND THE ... -

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Basic information

Entry
Database: PDB / ID: 2enb
TitleCRYSTAL STRUCTURES OF THE BINARY CA2+ AND PDTP COMPLEXES AND THE TERNARY COMPLEX OF THE ASP 21->GLU MUTANT OF STAPHYLOCOCCAL NUCLEASE. IMPLICATIONS FOR CATALYSIS AND LIGAND BINDING
ComponentsSTAPHYLOCOCCAL NUCLEASE
KeywordsHYDROLASE(PHOSPHORIC DIESTER)
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
THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.05 Å
AuthorsLibson, A. / Gittis, A. / Lattman, E.E.
CitationJournal: Biochemistry / Year: 1994
Title: Crystal structures of the binary Ca2+ and pdTp complexes and the ternary complex of the Asp21-->Glu mutant of staphylococcal nuclease. Implications for catalysis and ligand binding.
Authors: Libson, A.M. / Gittis, A.G. / Lattman, E.E.
History
DepositionMar 23, 1994Processing site: BNL
Revision 1.0May 31, 1994Provider: 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 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: STAPHYLOCOCCAL NUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8242
Polymers15,4221
Non-polymers4021
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.770, 48.770, 63.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Atom site foot note1: CIS PROLINE - PRO 117

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Components

#1: Protein STAPHYLOCOCCAL NUCLEASE


Mass: 15421.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / References: UniProt: P00644, micrococcal nuclease
#2: Chemical ChemComp-THP / THYMIDINE-3',5'-DIPHOSPHATE


Type: DNA linking / Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: NUC_ ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: NUC_STAAU SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ASP 103 GLU 21 SWISS-PROT PDB SEQRES COMMENT CONFLICT ASP 103 GLU 21 MUTATION SITE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 mg/mlD21E protein solution1drop
250 mMTES1reservoir
310 mMpdTp1reservoir
432-34 %(v/v)MPD1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 6 Å / Num. obs: 8297 / % possible obs: 80 % / Num. measured all: 37566 / Rmerge(I) obs: 0.043

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.177 / Rfactor obs: 0.177 / Highest resolution: 2.05 Å
Details: IN THE BINARY COMPLEX OF THE ASP 21 GLU MUTANT OF OF STAPHYLOCOCCAL NUCLEASE, A WATER MOLECULE REPLACES CA2+ AT THE ACTIVE SITE. THERE IS 0.5 ANGSTROMS MOVEMENT OF THE INHIBITOR, PDTP, AWAY ...Details: IN THE BINARY COMPLEX OF THE ASP 21 GLU MUTANT OF OF STAPHYLOCOCCAL NUCLEASE, A WATER MOLECULE REPLACES CA2+ AT THE ACTIVE SITE. THERE IS 0.5 ANGSTROMS MOVEMENT OF THE INHIBITOR, PDTP, AWAY FROM THE ACTIVE SITE. THE SIDE CHAIN OF GLU 43 POINTS INTO BULK SOLVENT.
Refinement stepCycle: LAST / Highest resolution: 2.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1094 0 25 43 1162
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg3.7
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
Refinement
*PLUS
Lowest resolution: 6 Å / Num. reflection obs: 7556 / Rfactor obs: 0.177 / Rfactor Rwork: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.7
X-RAY DIFFRACTIONx_chiral_restr0.116

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