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- PDB-1t8y: Crystal Structure of E.coli AMP Nucleosidase complexed with phosphate -

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Basic information

Entry
Database: PDB / ID: 1t8y
TitleCrystal Structure of E.coli AMP Nucleosidase complexed with phosphate
ComponentsAMP nucleosidase
KeywordsHYDROLASE / ALPHA-BETA-ALPHA SANDWICH / ALPHA-BETA FOLD
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
PHOSPHATE ION / AMP nucleosidase / AMP nucleosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhang, Y. / Cottet, S.E. / Ealick, S.E.
CitationJournal: STRUCTURE / Year: 2004
Title: Structure of Escherichia coli AMP Nucleosidase Reveals Similarity to Nucleoside Phosphorylases
Authors: Zhang, Y. / Cottet, S.E. / Ealick, S.E.
History
DepositionMay 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: AMP nucleosidase
B: AMP nucleosidase
C: AMP nucleosidase
D: AMP nucleosidase
E: AMP nucleosidase
F: AMP nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,03512
Polymers325,4666
Non-polymers5706
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30830 Å2
ΔGint-98 kcal/mol
Surface area94910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)268.500, 268.500, 114.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein
AMP nucleosidase


Mass: 54244.273 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: AMN, B1982, Z3139, ECS2779 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P15272, UniProt: P0AE12*PLUS, AMP nucleosidase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.3 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: ammonium formate, sodium chloride, ammonium phosphate, ethylene glycol, sodium citrate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 81165 / Num. obs: 78160 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3→3.19 Å / % possible all: 89.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→34.07 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 254824.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3919 5 %RANDOM
Rwork0.221 ---
all0.221 ---
obs0.221 78160 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.6329 Å2 / ksol: 0.293073 e/Å3
Displacement parametersBiso mean: 82.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.27 Å20 Å20 Å2
2--5.27 Å20 Å2
3----10.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.72 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 3→34.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21888 0 30 87 22005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.412 567 4.7 %
Rwork0.376 11450 -
obs--89.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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