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- PDB-4z8q: CRYSTAL STRUCTURE OF AvrRxo1-ORF1:AvrRxo1-ORF2 COMPLEX, SELENOMET... -

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Basic information

Entry
Database: PDB / ID: 4z8q
TitleCRYSTAL STRUCTURE OF AvrRxo1-ORF1:AvrRxo1-ORF2 COMPLEX, SELENOMETHIONINE SUBSTITUTED.
Components
  • AvrRxo1-ORF1
  • AvrRxo1-ORF2
KeywordsPROTEIN BINDING / AVRRXO1-ORF2 AVRRXO1-ORF1 AVRRXO1 AVRRXO1 REQUIRED CHAPERONE 1 / EFFECTOR PROTEINS AND MOLECULAR CHAPERONE
Function / homologyZeta toxin domain / Zeta toxin / kinase activity / P-loop containing nucleoside triphosphate hydrolase / ATP binding / PHOSPHATE ION / AvrRxo1-ORF1 / AvrRxo1-ORF2
Function and homology information
Biological speciesXanthomonas oryzae pv. oryzicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89 Å
AuthorsHan, Q. / Zhou, C. / Wu, S. / Liu, Y. / Yang, Z. / Miao, J. / Triplett, L. / Cheng, Q. / Tokuhisa, J. / Deblais, L. ...Han, Q. / Zhou, C. / Wu, S. / Liu, Y. / Yang, Z. / Miao, J. / Triplett, L. / Cheng, Q. / Tokuhisa, J. / Deblais, L. / Robinson, H. / Leach, J.E. / Li, J. / Zhao, B.
Funding support United States, China, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS-0845283 United States
United States Department of Agriculture (USDA), National Institute of Food and Agriculture (NIFA, United States)2011-67012-30570 United States
United States Department of Agriculture (USDA), National Institute of Food and Agriculture (NIFA, United States)2014-67013-21564 United States
National Natural Science Foundation of China (NSFC)31472186 China
CitationJournal: Structure / Year: 2015
Title: Crystal Structure of Xanthomonas AvrRxo1-ORF1, a Type III Effector with a Polynucleotide Kinase Domain, and Its Interactor AvrRxo1-ORF2.
Authors: Han, Q. / Zhou, C. / Wu, S. / Liu, Y. / Triplett, L. / Miao, J. / Tokuhisa, J. / Deblais, L. / Robinson, H. / Leach, J.E. / Li, J. / Zhao, B.
History
DepositionApr 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 16, 2022Group: Author supporting evidence / Data collection / Database references
Category: database_2 / diffrn_radiation_wavelength / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AvrRxo1-ORF1
B: AvrRxo1-ORF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3027
Polymers47,8272
Non-polymers4755
Water5,891327
1
A: AvrRxo1-ORF1
B: AvrRxo1-ORF2
hetero molecules

A: AvrRxo1-ORF1
B: AvrRxo1-ORF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,60414
Polymers95,6544
Non-polymers95010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area8830 Å2
ΔGint-48 kcal/mol
Surface area37600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.589, 88.869, 153.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-502-

PO4

21A-717-

HOH

31A-851-

HOH

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Components

#1: Protein AvrRxo1-ORF1


Mass: 36303.531 Da / Num. of mol.: 1 / Fragment: unp residues 90-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzicola (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q6TKR8
#2: Protein AvrRxo1-ORF2


Mass: 11523.586 Da / Num. of mol.: 1 / Fragment: unp residues 1-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzicola (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q6TKR9
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.69 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8 M NAH2PO4, 0.8 M KH2PO4, 15% GLYCEROL, 8 MM DTT, 0.1 M HEPES, , PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2012
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 39222 / % possible obs: 86 % / Observed criterion σ(I): 1 / Redundancy: 13.9 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 26.2
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 7.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: SAD / Resolution: 1.89→46.06 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2081 5 %RANDOM
Rwork0.226 ---
obs0.229 39222 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.89→46.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 25 327 3665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193389
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9884573
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3085424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08724150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83715593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5691526
X-RAY DIFFRACTIONr_chiral_restr0.0750.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212521
X-RAY DIFFRACTIONr_gen_planes_other
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.64 146 -
Rwork0.619 2458 -
obs--85.55 %

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