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- PDB-1ybf: Crystal structure of AMP nucleosidase from Bacteroides thetaiotao... -

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Basic information

Entry
Database: PDB / ID: 1ybf
TitleCrystal structure of AMP nucleosidase from Bacteroides thetaiotaomicron VPI-5482
ComponentsAMP nucleosidase
KeywordsHYDROLASE / Structural genomics / Protein Structure Initiative / PSI / New York SGX Research Center for Structural Genomics / NYSGXRC / T1840 / AMP nucleosidase / Bacteroides thetaiotaomicron
Function / homology
Function and homology information


AMP nucleosidase activity / nucleoside metabolic process / AMP salvage
Similarity search - Function
AMP nucleosidase, putative / AMP nucleosidase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AMP nucleosidase, putative
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsKrishnamurthy, N.R. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Crystal structure of AMP nucleosidase from Bacteroides thetaiotaomicron
Authors: Krishnamurthy, N.R. / Swaminathan, S.
History
DepositionDec 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 3, 2021Group: Derived calculations / Structure summary / Category: audit_author / struct_conn
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Remark 999SEQUENCE CHAINS A,B,C: RESIDUES 1-3:CLONING ARTIFACTS RESIDUES 261-268: HIS TAGS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMP nucleosidase
B: AMP nucleosidase
C: AMP nucleosidase


Theoretical massNumber of molelcules
Total (without water)91,9583
Polymers91,9583
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: AMP nucleosidase
B: AMP nucleosidase
C: AMP nucleosidase

A: AMP nucleosidase
B: AMP nucleosidase
C: AMP nucleosidase


Theoretical massNumber of molelcules
Total (without water)183,9156
Polymers183,9156
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_755-x+2,y,-z1
Buried area14630 Å2
ΔGint-84 kcal/mol
Surface area51560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)108.120, 108.120, 160.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein AMP nucleosidase


Mass: 30652.574 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7MVU1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.5 M Magnesium formate, Bis-Tris buffer, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 29, 2004 / Details: Mirrors
RadiationMonochromator: Silicone / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 26147 / Num. obs: 26147 / % possible obs: 97 % / Redundancy: 6 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 11
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 5 % / Rmerge(I) obs: 0.35 / Num. unique all: 2100 / Rsym value: 0.35 / % possible all: 95

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Processing

Software
NameVersionClassification
CBASSdata collection
SCALEPACKdata scaling
SOLVE& SHARPphasing
CNS1refinement
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2641 1021 -Random
Rwork0.2281 ---
all-21834 --
obs-21834 95 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.186 Å20 Å20 Å2
2--3.186 Å20 Å2
3----6.372 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5455 0 0 16 5471
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.32623
X-RAY DIFFRACTIONc_bond_d0.00703
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ion.param

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