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- PDB-4p5f: The crystal structure of type III effector protein XopQ complexed... -

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Basic information

Entry
Database: PDB / ID: 4p5f
TitleThe crystal structure of type III effector protein XopQ complexed with adenosine diphosphate ribose
ComponentsInosine-uridine nucleoside N-ribohydrolase
KeywordsHYDROLASE / Adenosine diphosphate ribose Complex Rossmann fold
Function / homology
Function and homology information


: / hydrolase activity, hydrolyzing N-glycosyl compounds / nucleobase-containing compound metabolic process / metal ion binding
Similarity search - Function
Inosine-uridine Nucleoside N-ribohydrolase; Chain A / Ribonucleoside hydrolase-like / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-AR6 / Inosine-uridine nucleoside N-ribohydrolase
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.1 Å
AuthorsYu, S. / Hwang, I. / Rhee, S.
CitationJournal: Proteins / Year: 2014
Title: The crystal structure of type III effector protein XopQ from Xanthomonas oryzae complexed with adenosine diphosphate ribose.
Authors: Yu, S. / Hwang, I. / Rhee, S.
History
DepositionMar 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inosine-uridine nucleoside N-ribohydrolase
B: Inosine-uridine nucleoside N-ribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9266
Polymers83,2472
Non-polymers6804
Water3,387188
1
A: Inosine-uridine nucleoside N-ribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6642
Polymers41,6231
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Inosine-uridine nucleoside N-ribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2634
Polymers41,6231
Non-polymers6393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.999, 73.808, 201.943
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Inosine-uridine nucleoside N-ribohydrolase


Mass: 41623.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria)
Strain: KACC10331 / KXO85 / Gene: URH1, XOO4466 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5GUA3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 8.5% (w/v) PEG 1000, 8.5% (w/v) PEG 8000, 15% (v/v) glycerol, 10 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 42892 / % possible obs: 99.8 % / Redundancy: 12.7 % / Biso Wilson estimate: 26.18 Å2 / Rmerge(I) obs: 0.153 / Χ2: 1.114 / Net I/av σ(I): 18.9 / Net I/σ(I): 5.6 / Num. measured all: 543348
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.1812.90.85642170.925100
2.18-2.2612.80.65741980.981100
2.26-2.3712.80.54142390.979100
2.37-2.4912.70.41242321.00299.9
2.49-2.6512.70.32942631.026100
2.65-2.8512.60.2542501.06899.5
2.85-3.1412.60.17642531.14799.7
3.14-3.5912.50.11942891.28599.5
3.59-4.5212.50.09243591.41899.7
4.52-5012.70.07645921.29599.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementResolution: 2.1→36.303 Å / FOM work R set: 0.8154 / SU ML: 0.27 / σ(F): 0 / Phase error: 25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2531 1943 4.73 %
Rwork0.2016 39148 -
obs0.204 41091 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.31 Å2 / Biso mean: 22.87 Å2 / Biso min: 6.86 Å2
Refinement stepCycle: final / Resolution: 2.1→36.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5357 0 39 188 5584
Biso mean--25.32 20.6 -
Num. residues----700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075510
X-RAY DIFFRACTIONf_angle_d1.1167513
X-RAY DIFFRACTIONf_chiral_restr0.071880
X-RAY DIFFRACTIONf_plane_restr0.005975
X-RAY DIFFRACTIONf_dihedral_angle_d13.952039
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0996-2.15210.31441340.23282551268590
2.1521-2.21030.30891310.23192603273491
2.2103-2.27530.31931290.21352653278292
2.2753-2.34880.29721310.21612680281194
2.3488-2.43270.26821360.21242726286294
2.4327-2.53010.28131420.21252762290495
2.5301-2.64520.29061380.21152740287896
2.6452-2.78460.28161380.23212777291596
2.7846-2.9590.28291420.22642834297697
2.959-3.18730.30681420.23112876301898
3.1873-3.50790.24071390.20882890302999
3.5079-4.01490.22051420.18452942308499
4.0149-5.05620.19621460.159929733119100
5.0562-36.30820.21641530.188931413294100

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