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- PDB-4ppu: Crystal Structure of AtCM1 with Tyrosine Bound in Allosteric Site -

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Basic information

Entry
Database: PDB / ID: 4ppu
TitleCrystal Structure of AtCM1 with Tyrosine Bound in Allosteric Site
ComponentsChorismate mutase 1, chloroplastic
KeywordsISOMERASE / Chorismate Mutase II / Mutase
Function / homology
Function and homology information


prephenate(2-) biosynthetic process / L-ascorbate peroxidase activity / chorismate metabolic process / chorismate mutase / chorismate mutase activity / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / chloroplast / protein homodimerization activity / cytosol
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 speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWestfall, C.S. / Xu, A. / Jez, J.M.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural evolution of differential amino Acid effector regulation in plant chorismate mutases.
Authors: Westfall, C.S. / Xu, A. / Jez, J.M.
History
DepositionFeb 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chorismate mutase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8182
Polymers31,6371
Non-polymers1811
Water2,342130
1
A: Chorismate mutase 1, chloroplastic
hetero molecules

A: Chorismate mutase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6374
Polymers63,2742
Non-polymers3622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3790 Å2
ΔGint-17 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.859, 99.859, 156.277
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-539-

HOH

21A-622-

HOH

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Components

#1: Protein Chorismate mutase 1, chloroplastic / / AtCM1 / CM-1


Mass: 31637.062 Da / Num. of mol.: 1 / Fragment: UNP residues 65-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CM1, At3g29200, MXO21.4 / Plasmid: pET28.a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42738, chorismate mutase
#2: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG-400, HEPES 7.5, 0.2 M MgCl2 hexahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 76 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2013
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→41.7 Å / Num. all: 13787 / Num. obs: 13649 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 32 % / Rsym value: 0.095 / Net I/σ(I): 14.4
Reflection shellResolution: 2.3→2.37 Å / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 6.6 / Num. unique all: 1344 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4CSM

4csm


Resolution: 2.3→41.7 Å / SU ML: 0.29 / σ(F): 1.37 / Phase error: 20.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 1365 10.01 %Random
Rwork0.1617 ---
obs0.167 13638 99.8 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.275 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.1599 Å20 Å2-0 Å2
2--3.1599 Å20 Å2
3----6.3198 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1975 0 13 130 2118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072032
X-RAY DIFFRACTIONf_angle_d1.0732744
X-RAY DIFFRACTIONf_dihedral_angle_d12.744775
X-RAY DIFFRACTIONf_chiral_restr0.072296
X-RAY DIFFRACTIONf_plane_restr0.005354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.37810.27071340.18821210X-RAY DIFFRACTION99
2.3781-2.47330.27361340.17791198X-RAY DIFFRACTION100
2.4733-2.58590.25511350.19251221X-RAY DIFFRACTION100
2.5859-2.72220.24341340.17511203X-RAY DIFFRACTION100
2.7222-2.89270.23131360.18371226X-RAY DIFFRACTION100
2.8927-3.1160.21841350.171217X-RAY DIFFRACTION100
3.116-3.42940.24971370.16811229X-RAY DIFFRACTION100
3.4294-3.92540.19261370.14511234X-RAY DIFFRACTION100
3.9254-4.94430.15981380.12441241X-RAY DIFFRACTION100
4.9443-41.70.19941450.16821294X-RAY DIFFRACTION99
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)
11.3622-0.4282-0.57850.12320.173.20310.01880.01910.21290.10490.1134-0.0706-0.01110.3059-0.15310.15320.01280.00630.17710.02010.253127.544835.37282.9742
28.1446-1.9216-6.09192.16362.73856.73040.2899-0.5225-0.134-0.17770.0764-0.0229-0.78450.9392-0.43590.2126-0.07780.02230.26530.00760.182132.03346.18212.7521
36.5146-3.7659-5.28474.3941.63796.3629-0.2194-0.2201-0.0172-0.04620.07740.11050.01980.94840.17280.1471-0.0227-0.04670.2753-0.01480.085329.074441.910112.96
45.7887-1.7301-1.1476.4641-1.00064.39930.2685-0.20580.67410.1904-0.0574-0.0278-0.66320.453-0.28640.2049-0.0138-0.01580.2424-0.08550.111225.827847.945217.5804
50.79280.3509-1.01240.1699-0.62942.9319-0.1246-0.1751-0.12380.0736-0.0724-0.11170.16730.60740.12160.15260.09260.00610.29470.01750.226432.215431.59728.0135
66.02290.33871.61241.4905-0.12252.32420.2019-0.2342-0.5542-0.1411-0.1589-0.3310.81720.8578-0.16160.45160.2385-0.02820.45780.11510.294832.845620.566329.3053
75.7168-2.16343.00035.4233-4.88558.6747-0.0444-0.0889-0.5443-0.13080.0678-0.52481.25920.02980.00460.44260.03560.0460.177-0.00380.415721.859316.20055.8452
87.65510.2516.12814.1944-1.048.42810.15660.4745-0.5521-0.32730.01120.11871.18450.2062-0.250.34120.08570.1020.2294-0.03210.330926.90318.6709-2.8585
93.4936-2.3443-2.45714.06211.49857.51880.0776-0.07980.2301-0.1875-0.2691-0.38360.04270.6970.14810.14590.091-0.01050.36860.05820.262832.688827.857223.554
107.6572-5.4076-4.13917.88796.41858.64920.13290.4125-0.0762-0.1076-0.0703-0.11810.0220.097-0.03430.12470.0605-0.05020.50570.00810.204520.54545.311.8983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 79:132 )A79 - 132
2X-RAY DIFFRACTION2(CHAIN A AND RESID 133:148)A133 - 148
3X-RAY DIFFRACTION3(CHAIN A AND RESID 149:160)A149 - 160
4X-RAY DIFFRACTION4(CHAIN A AND RESID 161:178)A161 - 178
5X-RAY DIFFRACTION5(CHAIN A AND RESID 179:243)A179 - 243
6X-RAY DIFFRACTION6(CHAIN A AND RESID 244:266)A244 - 266
7X-RAY DIFFRACTION7(CHAIN A AND RESID 267:284)A267 - 284
8X-RAY DIFFRACTION8(CHAIN A AND RESID 285:323)A285 - 323
9X-RAY DIFFRACTION9(CHAIN A AND RESID 324:340)A324 - 340
10X-RAY DIFFRACTION10(CHAIN A AND RESID 401:401)A401

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