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- PDB-1byr: CRYSTAL STRUCTURE OF A PHOSPHOLIPASE D FAMILY MEMBER, NUC FROM SA... -

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Basic information

Entry
Database: PDB / ID: 1byr
TitleCRYSTAL STRUCTURE OF A PHOSPHOLIPASE D FAMILY MEMBER, NUC FROM SALMONELLA TYPHIMURIUM
ComponentsPROTEIN (ENDONUCLEASE)
KeywordsENDONUCLEASE / PHOSPHODIESTERASE
Function / homology
Function and homology information


phosphorus metabolic process / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / phospholipase D / lipid catabolic process
Similarity search - Function
: / Phospholipase D-like domain / PLD-like domain / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / Endonuclease Chain A / Endonuclease; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2 Å
AuthorsStuckey, J.A. / Dixon, J.E.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Crystal structure of a phospholipase D family member.
Authors: Stuckey, J.A. / Dixon, J.E.
History
DepositionOct 19, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: PROTEIN (ENDONUCLEASE)


Theoretical massNumber of molelcules
Total (without water)17,1751
Polymers17,1751
Non-polymers00
Water3,387188
1
A: PROTEIN (ENDONUCLEASE)

A: PROTEIN (ENDONUCLEASE)


Theoretical massNumber of molelcules
Total (without water)34,3512
Polymers34,3512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2400 Å2
ΔGint-10 kcal/mol
Surface area11690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.060, 59.060, 111.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN (ENDONUCLEASE)


Mass: 17175.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cellular location: PERIPLASM / Gene: NUC / Plasmid: PT7-7 / Species (production host): Escherichia coli / Cellular location (production host): PERIPLASM / Gene (production host): NUC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q46707
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.5
Details: 10 MG/ML PROTEIN + 2M NH4SO4, 100MM TRIS-HCL,PH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Zhao, Y., (1997) Protein Sci., 6, 2655.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
21 Mammonium sulfate1drop
350 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: ADSC
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→16.4 Å / Num. obs: 13546 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.39 / Net I/σ(I): 15
Reflection shellResolution: 2→2.15 Å / Redundancy: 3 % / Mean I/σ(I) obs: 5.8 / Rsym value: 0.082 / % possible all: 96
Reflection
*PLUS
Num. measured all: 42490 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 96 % / Rmerge(I) obs: 0.082

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.851refinement
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1320 10.06 %RANDOM
Rwork0.193 ---
obs0.193 13112 95.8 %-
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 0 188 1369
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.61
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.72
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.757
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
LS refinement shellResolution: 2→2.15 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2344 136 10.3 %
Rwork0.2179 1390 -
obs--91.48 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH19.PEP
X-RAY DIFFRACTION3TOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 10.06 % / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.72
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.757
LS refinement shell
*PLUS
Highest resolution: 2 Å / % reflection Rfree: 10.3 % / Rfactor obs: 0.218

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