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- PDB-6fpf: Structure of the Ustilago maydis chorismate mutase 1 -

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Basic information

Entry
Database: PDB / ID: 6fpf
TitleStructure of the Ustilago maydis chorismate mutase 1
ComponentsChromosome 16, whole genome shotgun sequence
KeywordsCELL INVASION / Chorismate / Zea mays / smut disease
Function / homology
Function and homology information


effector-mediated suppression of host salicylic acid-mediated innate immune signaling / host apoplast / chorismate metabolic process / chorismate mutase / chorismate mutase activity / aromatic amino acid family biosynthetic process / host cell cytosol / extracellular region
Similarity search - Function
Chorismate mutase, AroQ class superfamily, eukaryotic / Chorismate mutase type II superfamily
Similarity search - Domain/homology
: / Secreted chorismate mutase
Similarity search - Component
Biological speciesUstilago maydis (corn smut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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 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 1.2Feb 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromosome 16, whole genome shotgun sequence
C: Chromosome 16, whole genome shotgun sequence
D: Chromosome 16, whole genome shotgun sequence
E: Chromosome 16, whole genome shotgun sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,2965
Polymers124,2414
Non-polymers551
Water15,043835
1
A: Chromosome 16, whole genome shotgun sequence
C: Chromosome 16, whole genome shotgun sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1753
Polymers62,1202
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-23 kcal/mol
Surface area24170 Å2
MethodPISA
2
D: Chromosome 16, whole genome shotgun sequence
E: Chromosome 16, whole genome shotgun sequence


Theoretical massNumber of molelcules
Total (without water)62,1202
Polymers62,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-22 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.768, 83.478, 186.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22D
13A
23E
14C
24D
15C
25E
16D
26E

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYCYSCYSAA31 - 28416 - 269
21GLYGLYCYSCYSCB31 - 28416 - 269
12GLUGLUTHRTHRAA29 - 28514 - 270
22GLUGLUTHRTHRDC29 - 28514 - 270
13ALAALACYSCYSAA30 - 28415 - 269
23ALAALACYSCYSED30 - 28415 - 269
14GLYGLYCYSCYSCB31 - 28416 - 269
24GLYGLYCYSCYSDC31 - 28416 - 269
15GLYGLYCYSCYSCB31 - 28416 - 269
25GLYGLYCYSCYSED31 - 28416 - 269
16ALAALACYSCYSDC30 - 28415 - 269
26ALAALACYSCYSED30 - 28415 - 269

NCS ensembles :
ID
1
2
3
4
5
6

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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: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 835 / 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: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M MES pH 5.0, 20 % (v/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: May 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.895→50.01 Å / Num. all: 102814 / Num. obs: 63072 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.1
Reflection shellResolution: 1.895→1.963 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 9715 / CC1/2: 0.71 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→49.74 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.2 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.2 / ESU R Free: 0.171 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 3375 5.1 %RANDOM
Rwork0.15539 ---
obs0.15775 63072 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.874 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--0.85 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 2.2→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8071 0 1 837 8909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0198288
X-RAY DIFFRACTIONr_bond_other_d0.0020.027833
X-RAY DIFFRACTIONr_angle_refined_deg2.4191.97111293
X-RAY DIFFRACTIONr_angle_other_deg1.259318176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68951035
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52823.777376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.744151429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4261573
X-RAY DIFFRACTIONr_chiral_restr0.1570.21335
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0219146
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021611
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_it2.7552.5464131
X-RAY DIFFRACTIONr_mcbond_other2.7532.5454130
X-RAY DIFFRACTIONr_mcangle_it4.0473.7895169
X-RAY DIFFRACTIONr_mcangle_other4.0473.7915170
X-RAY DIFFRACTIONr_scbond_it3.9183.14157
X-RAY DIFFRACTIONr_scbond_other3.9173.1024158
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2164.4416125
X-RAY DIFFRACTIONr_long_range_B_refined8.05732.239756
X-RAY DIFFRACTIONr_long_range_B_other7.99131.6229513
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.87

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A20185.21
22A20394.03
33A20216.42
44C20155.9
55C20134.9
66D20126.45
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 257 -
Rwork0.156 4585 -
obs--100 %
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)
10.29690.12190.09480.60590.0670.8708-0.01260.05350.0068-0.09780.038-0.0172-0.00440.0084-0.02550.03470.00290.02160.01650.00240.03442.289521.600536.1585
20.548-0.0338-0.31160.7445-0.10860.86760.0127-0.1038-0.02940.13860.0161-0.04240.0273-0.0327-0.02870.0592-0.0022-0.00150.03930.01020.0175-1.557714.056369.2257
30.4244-0.0258-0.16790.3387-0.0640.9596-0.0010.05440.0097-0.0707-0.02210.0443-0.04860.03510.02310.03860.0024-0.00150.013-0.0040.040342.389923.793536.4028
40.63410.09070.30260.93950.31481.71340.0051-0.1693-0.01880.1984-0.00910.02820.0869-0.07290.0040.06050.00620.02380.04660.00950.018741.561716.204769.4793
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 285
2X-RAY DIFFRACTION2C31 - 285
3X-RAY DIFFRACTION3D29 - 285
4X-RAY DIFFRACTION4E30 - 285

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