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- PDB-4z4a: Avirulence protein 4 (Avr4) from Pseudocercospora fuligena -

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Basic information

Entry
Database: PDB / ID: 4z4a
TitleAvirulence protein 4 (Avr4) from Pseudocercospora fuligena
ComponentsCarbohydrate-binding module family 14 protein
KeywordsSUGAR BINDING PROTEIN / Effector protein / Avirulence protein / CBM-14
Function / homologyChitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / chitin binding / extracellular region / Carbohydrate-binding module family 14 protein
Function and homology information
Biological speciesPseudocercospora fuligena (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsHurlburt, N.K. / Kohler, A.C. / Fisher, A.J.
Funding support United States, 1items
OrganizationGrant numberCountry
University of CaliforniaRI-091 United States
CitationJournal: Plant Cell / Year: 2016
Title: Structural Analysis of an Avr4 Effector Ortholog Offers Insight into Chitin Binding and Recognition by the Cf-4 Receptor.
Authors: Kohler, A.C. / Chen, L.H. / Hurlburt, N. / Salvucci, A. / Schwessinger, B. / Fisher, A.J. / Stergiopoulos, I.
History
DepositionApr 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Source and taxonomy
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Sep 14, 2016Group: Database references
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbohydrate-binding module family 14 protein
B: Carbohydrate-binding module family 14 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,77318
Polymers26,7802
Non-polymers99316
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-13 kcal/mol
Surface area8120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.100, 57.100, 126.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-313-

HOH

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Components

#1: Protein Carbohydrate-binding module family 14 protein


Mass: 13389.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudocercospora fuligena (fungus) / Plasmid: pPic9 / Production host: Komagataella pastoris GS115 (fungus) / Strain (production host): GS115 / References: UniProt: M3AZE0*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Ammonium sulfate (1.6-2.0M), 0.1M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 26958 / % possible obs: 99 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 17.9
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 2.61 / % possible all: 99.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→32.16 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.713 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20993 1362 5.1 %RANDOM
Rwork0.18285 ---
obs0.18422 25549 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.234 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 0 64 149 1349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021238
X-RAY DIFFRACTIONr_bond_other_d0.0010.021152
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.9851684
X-RAY DIFFRACTIONr_angle_other_deg0.8593.0132675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9065151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.726.1942
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66415181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211317
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02231
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_it1.6962.032598
X-RAY DIFFRACTIONr_mcbond_other1.6922.028597
X-RAY DIFFRACTIONr_mcangle_it2.5613.031745
X-RAY DIFFRACTIONr_mcangle_other2.5593.035746
X-RAY DIFFRACTIONr_scbond_it2.4912.456640
X-RAY DIFFRACTIONr_scbond_other2.4912.456640
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5443.416924
X-RAY DIFFRACTIONr_long_range_B_refined7.47318.8931494
X-RAY DIFFRACTIONr_long_range_B_other7.47118.9261495
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 94 -
Rwork0.26 1868 -
obs--99.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.99040.6192-0.18460.84060.35350.55030.0243-0.07480.09210.162-0.0470.12370.09380.06070.02270.1519-0.08870.02990.079-0.01680.1056-13.067615.11350.5068
21.01360.62020.31020.68480.37411.0179-0.04260.0483-0.02120.08580.02310.04690.14830.20520.01950.0872-0.00530.01220.09250.00040.0663-4.60768.6331-12.6168
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 104
2X-RAY DIFFRACTION2B32 - 106

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