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- PDB-2guw: Crystal structure of AMP Nucleosidase from Salmonella typhimurium LT2 -

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Basic information

Entry
Database: PDB / ID: 2guw
TitleCrystal structure of AMP Nucleosidase from Salmonella typhimurium LT2
ComponentsAMP nucleosidase
KeywordsHYDROLASE / AMP Nucleosidase / Molecular Replacement / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


AMP nucleosidase / AMP nucleosidase activity / nucleoside metabolic process / AMP salvage / cytosol
Similarity search - Function
amp nucleosidase, domain 1 / AMP nucleoside phosphorylase, N-terminal domain / AMP nucleosidase / AMP nucleoside phosphorylase, N-terminal / AMP nucleoside phosphorylase, N-terminal domain superfamily / Bacterial AMP nucleoside phosphorylase N-terminus / : / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily ...amp nucleosidase, domain 1 / AMP nucleoside phosphorylase, N-terminal domain / AMP nucleosidase / AMP nucleoside phosphorylase, N-terminal / AMP nucleoside phosphorylase, N-terminal domain superfamily / Bacterial AMP nucleoside phosphorylase N-terminus / : / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsRao, K.N. / 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 Salmonella typhimurium LT2
Authors: Rao, K.N. / Swaminathan, S.
History
DepositionMay 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 14, 2024Group: 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: AMP nucleosidase
B: AMP nucleosidase
C: AMP nucleosidase


Theoretical massNumber of molelcules
Total (without water)162,2033
Polymers162,2033
Non-polymers00
Water52229
1
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)324,4076
Polymers324,4076
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
MethodPQS
2
A: AMP nucleosidase
B: AMP nucleosidase


Theoretical massNumber of molelcules
Total (without water)108,1362
Polymers108,1362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-21 kcal/mol
Surface area34810 Å2
MethodPISA
3
C: AMP nucleosidase

C: AMP nucleosidase


Theoretical massNumber of molelcules
Total (without water)108,1362
Polymers108,1362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3390 Å2
ΔGint-12 kcal/mol
Surface area34440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.493, 170.284, 204.105
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsTrimer in the asymmetric unit but forms an hexamer via crystallographic symmetry

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Components

#1: Protein AMP nucleosidase


Mass: 54067.812 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZNS0, AMP nucleosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20-30% PEG MME550, 0.05M MgCl2, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2006 / Details: Mirrors
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. all: 59111 / Num. obs: 59111 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 52.1 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.4
Reflection shellResolution: 2.64→2.73 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.538 / Num. unique all: 5227 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→45.07 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 149607.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The residues listed in remark 465 are missing due to lack of electron density. For the atoms listed in remark 470 the relevant residues were modeled as Alanines since side chain density was ...Details: The residues listed in remark 465 are missing due to lack of electron density. For the atoms listed in remark 470 the relevant residues were modeled as Alanines since side chain density was absent. In general, the B factor seems to be high.
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1381 2.5 %RANDOM
Rwork0.244 ---
all0.265 55690 --
obs0.244 55690 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.1105 Å2 / ksol: 0.324631 e/Å3
Displacement parametersBiso mean: 76.1 Å2
Baniso -1Baniso -2Baniso -3
1-8.79 Å20 Å20 Å2
2---6.21 Å20 Å2
3----2.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.64→45.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9386 0 0 29 9415
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 2.64→2.81 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 181 2.4 %
Rwork0.369 7450 -
obs--77.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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