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- PDB-4tti: Crystal structure of double mutant E. Coli purine nucleoside phos... -

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Basic information

Entry
Database: PDB / ID: 4tti
TitleCrystal structure of double mutant E. Coli purine nucleoside phosphorylase with 4 FMC molecules
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsTRANSFERASE / Purine nucleoside phosphorylase / formicyn A
Function / homology
Function and homology information


purine nucleoside interconversion / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / DNA damage response / identical protein binding / membrane / cytosol
Similarity search - Function
Purine nucleoside phosphorylase DeoD-type / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FMC / PHOSPHATE ION / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsStefanic, Z. / Bzowska, A.
CitationJournal: Sci Rep / Year: 2018
Title: Crystallographic snapshots of ligand binding to hexameric purine nucleoside phosphorylase and kinetic studies give insight into the mechanism of catalysis.
Authors: Stefanic, Z. / Narczyk, M. / Mikleusevic, G. / Kazazic, S. / Bzowska, A. / Luic, M.
History
DepositionJun 21, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references / Structure summary
Revision 1.2Oct 31, 2018Group: Advisory / Data collection / Database references
Category: citation / citation_author / pdbx_unobs_or_zero_occ_residues
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 14, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.src_method / _entity_name_com.name ..._entity.src_method / _entity_name_com.name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
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: 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)155,66821
Polymers153,5496
Non-polymers2,11915
Water22,4651247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26020 Å2
ΔGint-224 kcal/mol
Surface area43870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.933, 124.174, 189.436
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a hexamer. One hexamer is found in asymmetric unit.

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Components

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


Mass: 25591.508 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: deoD, pup, b4384, JW4347 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0ABP8, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-FMC / (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol


Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1247 / 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: 2.4 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 50 mM citric buffer, 34 % ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97977 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97977 Å / Relative weight: 1
ReflectionResolution: 1.89→47.8 Å / Num. all: 757830 / Num. obs: 116237 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 26.915 Å2 / Rmerge F obs: 0.259 / Rmerge(I) obs: 0.169 / Rrim(I) all: 0.184 / Net I/σ(I): 10.89 / Num. measured all: 757830
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
1.89-21.411.2121.27527318822173641.368192.3
2-2.140.7430.8552.311271617675176640.9399.9
2.14-2.310.4830.5733.510891316495164910.622100
2.31-2.530.3180.3865.310383015199151950.417100
2.53-2.830.2080.25489778013857138550.274100
2.83-3.270.1150.14613.88914912254122520.157100
3.27-40.0540.07425.87698610421104210.08100
4-5.640.0320.04637.959919821682160.05100
5.640.0260.03443.333264479447790.03799.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1k9s

1k9s


Resolution: 1.89→47.7 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 5807 5 %random
Rwork0.1666 110329 --
obs0.1688 116136 98.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.2 Å2 / Biso mean: 21.377 Å2 / Biso min: 6.52 Å2
Refinement stepCycle: LAST / Resolution: 1.89→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10624 0 131 1247 12002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711042
X-RAY DIFFRACTIONf_angle_d1.16814922
X-RAY DIFFRACTIONf_chiral_restr0.0751703
X-RAY DIFFRACTIONf_plane_restr0.0041911
X-RAY DIFFRACTIONf_dihedral_angle_d14.1784038
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8903-1.91180.38591310.35482490262168
1.9118-1.93430.33891890.31593591378097
1.9343-1.95790.31890.26243594378399
1.9579-1.98270.29421940.2493683387799
1.9827-2.00880.29031950.236836953890100
2.0088-2.03630.25321930.219136683861100
2.0363-2.06540.25751960.207337223918100
2.0654-2.09620.24781910.20536403831100
2.0962-2.1290.26961940.198236773871100
2.129-2.16390.24551940.194936843878100
2.1639-2.20120.25711950.186437023897100
2.2012-2.24120.251940.184536843878100
2.2412-2.28430.23451950.172537073902100
2.2843-2.3310.21611940.167336843878100
2.331-2.38160.22991950.161937083903100
2.3816-2.4370.19991940.165537043898100
2.437-2.4980.22441940.164736853879100
2.498-2.56550.25931960.162937133909100
2.5655-2.6410.20941950.15837053900100
2.641-2.72620.2121960.148837313927100
2.7262-2.82370.23181970.154137373934100
2.8237-2.93670.1991950.152537023897100
2.9367-3.07030.18831970.151737363933100
3.0703-3.23220.17631960.143137373933100
3.2322-3.43460.17751980.130137643962100
3.4346-3.69970.16051960.125437333929100
3.6997-4.07190.13712000.124437943994100
4.0719-4.66060.13481990.115237983997100
4.6606-5.87020.21532030.158538494052100
5.8702-47.85030.21012120.188940124224100

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