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- PDB-4z8v: CRYSTAL STRUCTURE OF AVRRXO1-ORF1:-ORF2 COMPLEX, NATIVE. -

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Basic information

Entry
Database: PDB / ID: 4z8v
TitleCRYSTAL STRUCTURE OF AVRRXO1-ORF1:-ORF2 COMPLEX, NATIVE.
Components
  • AvrRxo1-ORF1
  • AvrRxo1-ORF2
KeywordsPROTEIN BINDING / TYPE III EFFECTOR PROTEINS / CHAPERONE
Function / homologyP-loop containing nucleoside triphosphate hydrolase / PHOSPHATE ION / AvrRxo1-ORF1 / AvrRxo1-ORF2
Function and homology information
Biological speciesXanthomonas oryzae pv. oryzicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
Revision 1.5Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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

Theoretical massNumber of molelcules
Total (without water)48,1578
Polymers47,5872
Non-polymers5706
Water2,810156
1
A: AvrRxo1-ORF1
B: AvrRxo1-ORF2
hetero molecules

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

Theoretical massNumber of molelcules
Total (without water)96,31316
Polymers95,1734
Non-polymers1,14012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area9170 Å2
ΔGint-57 kcal/mol
Surface area37790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.299, 88.390, 152.532
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-504-

PO4

21A-654-

HOH

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Components

#1: Protein AvrRxo1-ORF1

Mass: 36203.832 Da / Num. of mol.: 1 / Fragment: unp residues 88-421
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: 11382.900 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.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
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, PH7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2011
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: 2.3→50 Å / Num. obs: 21791 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.9

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Processing

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

4q5l
PDB Unreleased entry


Resolution: 2.3→45.82 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.918 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1176 5.1 %RANDOM
Rwork0.202 ---
obs0.204 21791 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 30 156 3511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193405
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9844596
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0455426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59724150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19815609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3671526
X-RAY DIFFRACTIONr_chiral_restr0.0760.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212529
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 91 -
Rwork0.244 1575 -
obs--98.87 %

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