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- PDB-6hjw: Crystal structure of the chloroplast chorismate mutase from Zea mays -

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Basic information

Entry
Database: PDB / ID: 6hjw
TitleCrystal structure of the chloroplast chorismate mutase from Zea mays
ComponentsChorismate mutase
KeywordsPLANT PROTEIN / chorismate mutase / zea mays / chloroplast
Function / homology
Function and homology information


chorismate metabolic process / chorismate mutase / chorismate mutase activity / aromatic amino acid family biosynthetic process / chloroplast / protein homodimerization activity
Similarity search - Function
Chorismate Mutase, subunit A / Chorismate mutase, AroQ class superfamily, eukaryotic / Chorismate mutase, AroQ class, eukaryotic type / Chorismate mutase domain profile. / Chorismate mutase, AroQ class superfamily, eukaryotic / Chorismate mutase type II superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TYROSINE / Chorismate mutase 1, chloroplastic
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAltegoer, F. / 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
DepositionSep 4, 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 ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Feb 13, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 2.0Oct 2, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _cell.Z_PDB / _pdbx_entity_nonpoly.entity_id ..._cell.Z_PDB / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _struct_asym.entity_id / _struct_ref_seq.ref_id
Revision 2.1Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chorismate mutase
B: Chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1534
Polymers70,7912
Non-polymers3622
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-24 kcal/mol
Surface area22260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.800, 89.830, 216.840
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
11B-249-

MET

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Components

#1: Protein Chorismate mutase /


Mass: 35395.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 100272431, ZEAMMB73_Zm00001d043356 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4FNK8, chorismate mutase
#2: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C9H11NO3 / References: UniProt: B4FNK8*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium tartrate, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.5→48.92 Å / Num. obs: 21328 / % possible obs: 99.5 % / Redundancy: 6.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.46
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.018 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 2101 / CC1/2: 0.81 / % possible all: 99.48

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CSM

3csm


Resolution: 2.5→46.086 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.63
RfactorNum. reflection% reflection
Rfree0.2741 1066 5.01 %
Rwork0.2226 --
obs0.2252 21328 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→46.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 26 19 3995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034059
X-RAY DIFFRACTIONf_angle_d0.5785487
X-RAY DIFFRACTIONf_dihedral_angle_d3.2272491
X-RAY DIFFRACTIONf_chiral_restr0.041598
X-RAY DIFFRACTIONf_plane_restr0.004709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.61380.36931290.33982459X-RAY DIFFRACTION100
2.6138-2.75160.42111310.30672473X-RAY DIFFRACTION99
2.7516-2.9240.31551320.29142502X-RAY DIFFRACTION100
2.924-3.14970.34941320.27562502X-RAY DIFFRACTION100
3.1497-3.46660.36931330.26372529X-RAY DIFFRACTION100
3.4666-3.96790.24541330.2192526X-RAY DIFFRACTION100
3.9679-4.99820.23071350.18122559X-RAY DIFFRACTION100
4.9982-46.09380.2321410.18872665X-RAY DIFFRACTION100
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)
16.2630.80850.15421.85830.11931.9661-0.048-0.25940.5271-0.2569-0.00950.4182-0.1785-0.49340.14990.59990.0016-0.04640.524-0.01830.42058.775828.378715.1277
25.07851.4113-2.45822.8106-0.58491.71310.1794-1.078-0.92760.6225-0.6403-0.67390.1190.39010.59010.5969-0.0458-0.14670.91660.1870.663829.200314.025131.0489
33.65321.35430.43650.771.29933.91190.1779-0.7925-0.50280.3712-0.2041-0.13161.1446-0.3447-0.01880.593-0.0469-0.05910.5960.18830.542810.858214.440625.2117
43.2183-0.7924-3.48642.0936-0.4595.3030.1562-0.7941-1.01970.594-0.5099-0.30250.7051-0.59040.06080.7503-0.4007-0.08340.75540.18640.7445-0.404513.608321.1368
56.7435-1.24832.56972.6950.24696.0180.1364-0.5093-0.75090.028-0.0301-0.18840.8264-0.0459-0.10990.45480.050.01340.36620.05860.351722.437716.30616.7547
64.01541.18835.07921.02283.1979.2509-0.04550.4178-0.2908-0.05830.1306-0.11860.05290.5945-0.03760.4299-0.04130.00780.29690.04750.43912.906618.63554.1225
74.04041.7641.2643.43221.09874.35060.09740.28630.2701-0.2446-0.1016-0.1373-0.24210.41460.04920.52330.02320.04360.48560.1160.423420.852126.97657.2057
82.1054-0.20251.12921.40190.87882.3749-0.0929-0.7582-0.13290.280.05380.02950.0653-0.26970.01640.4819-0.0249-0.00330.82390.05590.350613.179831.614336.1265
93.4446-0.28034.02991.62191.46248.3006-0.89220.10110.7544-0.04050.10830.4482-1.4633-0.41570.80870.8170.048-0.12810.73470.10040.528815.343250.235733.0644
103.07410.7110.67783.11670.46932.4225-0.1039-0.91590.16410.48570.0782-0.1226-0.2858-0.04090.00590.58610.1372-0.09460.8334-0.02290.47318.696542.881646.0285
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 78 through 111 )
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 160 )
4X-RAY DIFFRACTION4chain 'A' and (resid 161 through 178 )
5X-RAY DIFFRACTION5chain 'A' and (resid 179 through 211 )
6X-RAY DIFFRACTION6chain 'A' and (resid 212 through 266 )
7X-RAY DIFFRACTION7chain 'A' and (resid 267 through 333 )
8X-RAY DIFFRACTION8chain 'B' and (resid 79 through 243 )
9X-RAY DIFFRACTION9chain 'B' and (resid 244 through 315 )
10X-RAY DIFFRACTION10chain 'B' and (resid 316 through 501 )

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