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- PDB-6fpg: Structure of the Ustilago maydis chorismate mutase 1 in complex w... -

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Basic information

Entry
Database: PDB / ID: 6fpg
TitleStructure of the Ustilago maydis chorismate mutase 1 in complex with a Zea mays kiwellin
Components
  • Chromosome 16, whole genome shotgun sequence
  • Ripening-related protein 3
KeywordsCELL INVASION / Smut disease / kiwellin / chorismate
Function / homology
Function and homology information


host-mediated perturbation of symbiont process / effector-mediated suppression of host salicylic acid-mediated innate immune signaling / host apoplast / chorismate metabolic process / chorismate mutase / chorismate mutase activity / apoplast / aromatic amino acid family biosynthetic process / host cell cytosol / enzyme inhibitor activity ...host-mediated perturbation of symbiont process / effector-mediated suppression of host salicylic acid-mediated innate immune signaling / host apoplast / chorismate metabolic process / chorismate mutase / chorismate mutase activity / apoplast / aromatic amino acid family biosynthetic process / host cell cytosol / enzyme inhibitor activity / defense response to fungus / extracellular region
Similarity search - Function
Kiwellin-like / Chorismate mutase, AroQ class superfamily, eukaryotic / Chorismate mutase type II superfamily / RlpA-like domain superfamily
Similarity search - Domain/homology
CITRIC ACID / Secreted chorismate mutase / Kiwellin-1
Similarity search - Component
Biological speciesUstilago maydis (corn smut)
Zea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAltegoer, F. / Steinchen, W. / Bange, G.
CitationJournal: Nature / Year: 2019
Title: A kiwellin disarms the metabolic activity of a secreted fungal virulence factor.
Authors: Han, X. / Altegoer, F. / Steinchen, W. / Binnebesel, L. / Schuhmacher, J. / Glatter, T. / Giammarinaro, P.I. / Djamei, A. / Rensing, S.A. / Reissmann, S. / Kahmann, R. / Bange, G.
History
DepositionFeb 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Revision 1.2Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Feb 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Chromosome 16, whole genome shotgun sequence
B: Chromosome 16, whole genome shotgun sequence
D: Ripening-related protein 3
E: Ripening-related protein 3
F: Chromosome 16, whole genome shotgun sequence
G: Chromosome 16, whole genome shotgun sequence
H: Ripening-related protein 3
I: Ripening-related protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,10012
Polymers199,3318
Non-polymers7684
Water21,0961171
1
C: Chromosome 16, whole genome shotgun sequence
B: Chromosome 16, whole genome shotgun sequence
D: Ripening-related protein 3
E: Ripening-related protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0506
Polymers99,6664
Non-polymers3842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10140 Å2
ΔGint-18 kcal/mol
Surface area35830 Å2
MethodPISA
2
F: Chromosome 16, whole genome shotgun sequence
G: Chromosome 16, whole genome shotgun sequence
H: Ripening-related protein 3
I: Ripening-related protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0506
Polymers99,6664
Non-polymers3842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-21 kcal/mol
Surface area36290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.507, 85.660, 95.785
Angle α, β, γ (deg.)96.16, 92.39, 90.37
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Chromosome 16, whole genome shotgun sequence


Mass: 31060.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ustilago maydis (strain 521 / FGSC 9021) (fungus)
Gene: UMAG_05731 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D1DWQ2
#2: Protein
Ripening-related protein 3


Mass: 18772.604 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 103626138, ZEAMMB73_Zm00001d013945 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D6GNR3
#3: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1171 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M sodium citrate pH 5.5, 15 % (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→49 Å / Num. obs: 168279 / % possible obs: 96.6 % / Redundancy: 2.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.041 / Net I/σ(I): 11.2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 16605 / CC1/2: 0.7 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FPF

6fpf


Resolution: 1.8→48.497 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.08
RfactorNum. reflection% reflection
Rfree0.2164 8386 4.98 %
Rwork0.1865 --
obs0.188 168242 96.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→48.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12829 0 52 1172 14053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913157
X-RAY DIFFRACTIONf_angle_d1.20117886
X-RAY DIFFRACTIONf_dihedral_angle_d8.8438478
X-RAY DIFFRACTIONf_chiral_restr0.0632031
X-RAY DIFFRACTIONf_plane_restr0.0082359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.35373020.31865200X-RAY DIFFRACTION95
1.8205-1.84190.31182720.29825241X-RAY DIFFRACTION95
1.8419-1.86430.31982870.2825303X-RAY DIFFRACTION96
1.8643-1.88790.30512840.27315165X-RAY DIFFRACTION95
1.8879-1.91280.29952630.2655343X-RAY DIFFRACTION95
1.9128-1.9390.26712810.24875255X-RAY DIFFRACTION96
1.939-1.96670.28412780.23915305X-RAY DIFFRACTION96
1.9667-1.9960.28192990.2285338X-RAY DIFFRACTION96
1.996-2.02720.27332910.23855237X-RAY DIFFRACTION96
2.0272-2.06050.25613140.23395290X-RAY DIFFRACTION96
2.0605-2.0960.25692550.22755318X-RAY DIFFRACTION96
2.096-2.13410.28832710.23315390X-RAY DIFFRACTION97
2.1341-2.17520.27712440.22275334X-RAY DIFFRACTION97
2.1752-2.21960.26482930.21335305X-RAY DIFFRACTION96
2.2196-2.26780.24732900.21065244X-RAY DIFFRACTION96
2.2678-2.32060.25212780.21135320X-RAY DIFFRACTION96
2.3206-2.37860.24232950.20545400X-RAY DIFFRACTION97
2.3786-2.44290.23742880.20925282X-RAY DIFFRACTION97
2.4429-2.51480.23492880.20085380X-RAY DIFFRACTION97
2.5148-2.5960.22532900.19485378X-RAY DIFFRACTION97
2.596-2.68870.18962960.1915319X-RAY DIFFRACTION97
2.6887-2.79640.23723030.19215298X-RAY DIFFRACTION97
2.7964-2.92360.22892910.19325325X-RAY DIFFRACTION97
2.9236-3.07770.25432350.19385396X-RAY DIFFRACTION97
3.0777-3.27050.21782510.19615456X-RAY DIFFRACTION98
3.2705-3.5230.21792960.1815378X-RAY DIFFRACTION98
3.523-3.87740.16662600.16325415X-RAY DIFFRACTION98
3.8774-4.43810.16332490.14455363X-RAY DIFFRACTION97
4.4381-5.59030.17672610.14415471X-RAY DIFFRACTION99
5.5903-48.51450.16762810.14985407X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 30.9881 Å / Origin y: -6.8305 Å / Origin z: -14.7153 Å
111213212223313233
T0.1717 Å2-0.0365 Å2-0.0187 Å2-0.1694 Å20.0186 Å2--0.1921 Å2
L0.2914 °2-0.1992 °2-0.1585 °2-0.1999 °20.1617 °2--0.3472 °2
S-0.038 Å °0.0119 Å °-0.0149 Å °0.0074 Å °0.0487 Å °-0.0092 Å °0.0231 Å °-0.0107 Å °0.0002 Å °
Refinement TLS groupSelection details: all

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