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- PDB-4kl0: Crystal structure of the effector protein XOO4466 -

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Basic information

Entry
Database: PDB / ID: 4kl0
TitleCrystal structure of the effector protein XOO4466
ComponentsPutative uncharacterized protein
KeywordsCalcium Binding Protein / Rossmann Fold / Unknown Function
Function / homology
Function and homology information


hydrolase activity, hydrolyzing N-glycosyl compounds / 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
Inosine-uridine nucleoside N-ribohydrolase
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.598 Å
AuthorsYu, S. / Rhee, S.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Crystal structure of the effector protein XOO4466 from Xanthomonas oryzae
Authors: Yu, S. / Hwang, I. / Rhee, S.
History
DepositionMay 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _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

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1682
Polymers41,1281
Non-polymers401
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.832, 70.528, 49.083
Angle α, β, γ (deg.)90.00, 99.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein / Bacterial effector protein


Mass: 41127.898 Da / Num. of mol.: 1 / Fragment: UNP residues 110-485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria)
Strain: KACC10331 / Gene: XOO4466 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5GUA3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.98 Å3/Da / Density % sol: 37.97 % / Mosaicity: 0.292 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 8.5% PEG 8000, 8.5% PEG 1000, 15% glycerol, 10mM calcium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.9789, 0.9791, 0.9639
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 14, 2011
RadiationMonochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97911
30.96391
ReflectionResolution: 1.598→50 Å / Num. obs: 42434 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 18.75 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 26.284
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2.374 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.598→39.881 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.825 / SU ML: 0.47 / σ(F): 2 / Phase error: 25.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 1988 4.71 %RANDOM
Rwork0.2019 40202 --
obs0.2035 42190 99.23 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.062 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 57.73 Å2 / Biso mean: 22.165 Å2 / Biso min: 7.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.206 Å2-0 Å2-1.4836 Å2
2--3.6079 Å2-0 Å2
3----2.4018 Å2
Refinement stepCycle: LAST / Resolution: 1.598→39.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 1 176 2865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182741
X-RAY DIFFRACTIONf_angle_d1.7433731
X-RAY DIFFRACTIONf_chiral_restr0.11437
X-RAY DIFFRACTIONf_plane_restr0.009486
X-RAY DIFFRACTIONf_dihedral_angle_d14.2731015
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 (%)
1.5983-1.63830.32661350.27552807294297
1.6383-1.68260.28081420.26682835297799
1.6826-1.73210.33991410.25492828296999
1.7321-1.7880.31971370.24472853299099
1.788-1.85190.25321400.22552885302599
1.8519-1.9260.2631400.212830297099
1.926-2.01370.24531470.21052888303599
2.0137-2.11990.26561370.21128753012100
2.1199-2.25270.26681420.208928893031100
2.2527-2.42660.25911460.206828823028100
2.4266-2.67070.28351410.206628843025100
2.6707-3.05710.22951440.209529093053100
3.0571-3.85110.18551450.179329003045100
3.8511-39.89320.19281510.17412937308899

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