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- PDB-4rj2: Crystal structure of E.coli purine nucleoside phosphorylase at 0.... -

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Basic information

Entry
Database: PDB / ID: 4rj2
TitleCrystal structure of E.coli purine nucleoside phosphorylase at 0.99 A resolution
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsTRANSFERASE / phosphorylase
Function / homologyNucleoside phosphorylase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å
AuthorsTimofeev, V.I. / Abramchik, Y.A. / Esipov, R.S. / Kuranova, I.P.
CitationJournal: To be Published
Title: Crystal structure of E.coli purine nucleoside phosphorylase at 0.99 A resolution
Authors: Timofeev, V.I. / Abramchik, Y.A. / Esipov, R.S. / Kuranova, I.P.
History
DepositionOct 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / exptl_crystal_grow / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal_grow.method / _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

Downloads & links

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
D: Purine nucleoside phosphorylase DeoD-type
E: Purine nucleoside phosphorylase DeoD-type
F: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,88212
Polymers154,3306
Non-polymers5536
Water17,096949
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22460 Å2
ΔGint-123 kcal/mol
Surface area45710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.120, 110.220, 88.210
Angle α, β, γ (deg.)90.00, 111.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Purine nucleoside phosphorylase DeoD-type / PNP


Mass: 25721.633 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: deoD / Production host: Escherichia coli (E. coli)
References: UniProt: H0QGF5, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 949 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growMethod: counter-diffusion / Details: COUNTER DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.99→20 Å / Num. obs: 718472 / % possible obs: 98.41 % / Redundancy: 3.71 % / Rmerge(I) obs: 0.1
Reflection shellResolution: 0.99→1.04 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.11 / Num. unique all: 104431 / % possible all: 98.05

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.99→16.28 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18866 35993 5 %RANDOM
Rwork0.17558 ---
obs0.17623 682425 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.135 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.08 Å2
2---0.22 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 0.99→16.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10758 0 36 949 11743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01911509
X-RAY DIFFRACTIONr_bond_other_d00.0211218
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.96315565
X-RAY DIFFRACTIONr_angle_other_deg3.716325819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35951523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69223.594473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.662152022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5451579
X-RAY DIFFRACTIONr_chiral_restr0.2570.21772
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213212
X-RAY DIFFRACTIONr_gen_planes_other0.0090.022563
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr13.776322727
X-RAY DIFFRACTIONr_sphericity_free26.5915245
X-RAY DIFFRACTIONr_sphericity_bonded7.025523226
LS refinement shellResolution: 0.99→1.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 2590 -
Rwork0.329 50114 -
obs--97.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2598-0.20240.05850.18660.03550.2806-0.0164-0.04250.01830.02550.0282-0.02630.0125-0.012-0.01180.0501-0.006-0.01950.0152-0.00290.026413.385-4.49558.55
20.3122-0.1463-0.12110.22960.12150.42220.04950.0905-0.0008-0.0674-0.0641-0.0284-0.0362-0.02680.01460.06010.04790.00710.05620.01410.038116.907-9.2238.809
30.2789-0.2035-0.05720.17490.02980.19520.03920.01990.0147-0.0283-0.02620.0063-0.01580.0037-0.01290.04630.0079-0.00270.0109-0.00660.0318-21.04416.44428.929
40.2488-0.2064-0.03040.24470.02520.12530.00650.005-0.0008-0.0023-0.0178-0.03170.0101-0.00290.01130.03840.0067-0.00670.00530.00760.050825.629-16.82536.562
50.3135-0.2057-0.03860.16780.02610.1842-0.0121-0.04470.00610.01840.01140.01490.00890.00150.00060.0431-0.00670.00160.0212-0.01210.0244-12.9769.30154.977
60.2179-0.18210.00480.20680.03320.41450.07360.06-0.006-0.0633-0.0496-0.00520.0340.0139-0.0240.06680.0456-0.00580.0504-0.00250.0037-7.7933.6465.434
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 237
2X-RAY DIFFRACTION2B1 - 237
3X-RAY DIFFRACTION3C1 - 237
4X-RAY DIFFRACTION4D1 - 237
5X-RAY DIFFRACTION5E1 - 237
6X-RAY DIFFRACTION6F1 - 237

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