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- PDB-1ak0: P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG -

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Basic information

Entry
Database: PDB / ID: 1ak0
TitleP1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG
ComponentsP1 NUCLEASE
KeywordsENDONUCLEASE / P1 NUCLEASE / REACTION MECHANISM / THIOPHOSPHORYLATED OLIGONUCLEOTIDES / GLYCOSYLATED PROTEIN
Function / homologyS1/P1 nuclease / Phospholipase C/P1 nuclease domain superfamily / S1/P1 Nuclease / Aspergillus nuclease S1 / DNA catabolic process / endonuclease activity / nucleic acid binding / extracellular region / metal ion binding / Nuclease P1
Function and homology information
Specimen sourcePenicillium citrinum (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 1.8 Å resolution
AuthorsRomier, C. / Suck, D.
Citation
Journal: Proteins / Year: 1998
Title: Recognition of single-stranded DNA by nuclease P1: high resolution crystal structures of complexes with substrate analogs.
Authors: Romier, C. / Dominguez, R. / Lahm, A. / Dahl, O. / Suck, D.
#1: Journal: Embo J. / Year: 1991
Title: Crystal Structure of Penicillium Citrinum P1 Nuclease at 2.8 A Resolution
Authors: Volbeda, A. / Lahm, A. / Sakiyama, F. / Suck, D.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 28, 1997 / Release: Dec 3, 1997
RevisionDateData content typeGroupProviderType
1.0Dec 3, 1997Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P1 NUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,84013
Polyers29,2511
Non-polymers2,58912
Water2,774154
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)41.980, 74.040, 102.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide P1 NUCLEASE


Mass: 29251.021 Da / Num. of mol.: 1 / Source: (natural) Penicillium citrinum (fungus) / Genus: Penicillium / References: UniProt: P24289, Aspergillus nuclease S1

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Non-polymers , 5 types, 166 molecules

#2: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 4 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Formula: Zn / Zinc
#4: Chemical ChemComp-ADS / ADENOSINE-5'-(DITHIO)PHOSPHATE


Mass: 379.352 Da / Num. of mol.: 1 / Formula: C10H14N5O5PS2
#5: Chemical ChemComp-THS / THYMIDINE-5'-(DITHIO)PHOSPHATE


Mass: 354.340 Da / Num. of mol.: 3 / Formula: C10H15N2O6PS2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Formula: H2O / Water

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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: 2.71 / Density percent sol: 54.65 %
Crystal growpH: 5.3 / Details: PEG 6000 12 - 20% 25 MM NA ACETATE PH 5.3
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
10.8 mMprotein1drop
425 mMsodium acetate1reservoir
512-20 %(w/v)PEG60001reservoir
62 mMzinc chloride1reservoir
2DNA1drop
3reservoir1drop

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Data collection

DiffractionMean temperature: 293 kelvins
SourceType: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Jan 1, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 1.8 Å / D resolution low: 15 Å / Number obs: 27854 / Observed criterion sigma I: 2 / Rsym value: 0.068 / Redundancy: 4.3 % / Percent possible obs: 93.2
Reflection shellHighest resolution: 1.8 Å / Lowest resolution: 1.95 Å / Rsym value: 0.247 / Percent possible all: 89.9
Reflection
*PLUS
Number measured all: 119199 / Rmerge I obs: 0.068
Reflection shell
*PLUS
Percent possible obs: 89.9 / Rmerge I obs: 0.247

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT / R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0.001 / Sigma F: 2
Displacement parametersB iso mean: 22.8 Å2
Least-squares processR factor R free: 0.235 / R factor R work: 0.207 / R factor obs: 0.207 / Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Number reflection obs: 27019 / Percent reflection R free: 1 / Percent reflection obs: 89.1
Refine analyzeLuzzati d res low obs: 8 Å
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 2021 / Nucleic acid: 0 / Ligand: 138 / Solvent: 154 / Total: 2313
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.7
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_it1.5
X-RAY DIFFRACTIONx_mcangle_it2.0
X-RAY DIFFRACTIONx_scbond_it2.0
X-RAY DIFFRACTIONx_scangle_it2.5
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3.CHOTOPH3.CHO
X-RAY DIFFRACTION3PARNAH1E.DNATOPNAH1E.DNA
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Displacement parameters
*PLUS
B iso mean: 21.8 Å2

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