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- PDB-4z8u: CRYSTAL STRUCTURE OF AvrRxo1-ORF1:-ORF2 WITH ATP -

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Basic information

Entry
Database: PDB / ID: 4z8u
TitleCRYSTAL STRUCTURE OF AvrRxo1-ORF1:-ORF2 WITH ATP
Components
  • AvrRxo1-ORF1
  • AvrRxo1-ORF2
KeywordsPROTEIN BINDING / AVRRXO1-ORF2 AVRRXO1-ORF1 AVRRXO1 AVRRXO1 REQUIRED CHAPERONE 1 / EFFECTOR PROTEINS AND MOLECULAR CHAPERONE / ATP
Function / homologyZeta toxin domain / Zeta toxin / kinase activity / P-loop containing nucleoside triphosphate hydrolase / ATP binding / ACETATE ION / AvrRxo1-ORF1 / AvrRxo1-ORF2
Function and homology information
Biological speciesXanthomonas oryzae pv. oryzicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)48,4599
Polymers47,8272
Non-polymers6317
Water5,765320
1
A: AvrRxo1-ORF1
B: AvrRxo1-ORF2
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)96,91718
Polymers95,6544
Non-polymers1,26314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area10560 Å2
ΔGint-60 kcal/mol
Surface area35750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.225, 88.385, 152.709
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-648-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#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

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Non-polymers , 4 types, 327 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.6M (NH4)2SO4, 18% GLYCEROL, 8 MM DTT, 100 MM NA-CITRATE, 30 MM ATP AND 60 MM MAGNESIUM ACETATE, PH 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2012
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 58250 / % possible obs: 98.6 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.087 / Rsym value: 0.09 / Net I/σ(I): 20.1
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.771 / % possible all: 85.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PDB ENTRY Q5L

4pdb


Resolution: 1.65→45.82 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3119 5.1 %RANDOM
Rwork0.2 ---
obs0.202 58250 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.65→45.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3331 0 35 320 3686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0193416
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0431.994609
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4125428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.51624150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35215595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7931526
X-RAY DIFFRACTIONr_chiral_restr0.1690.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212541
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: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 221 -
Rwork0.335 3853 -
obs--90.67 %

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