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- PDB-4ppv: Crystal Structure of AtCM1 with Phenylalanine Bound in Allosteric Site -

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Basic information

Entry
Database: PDB / ID: 4ppv
TitleCrystal Structure of AtCM1 with Phenylalanine 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
PHENYLALANINE / Chorismate mutase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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)31,8022
Polymers31,6371
Non-polymers1651
Water1,49583
1
A: Chorismate mutase 1, chloroplastic
hetero molecules

A: Chorismate mutase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6054
Polymers63,2742
Non-polymers3302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3860 Å2
ΔGint-17 kcal/mol
Surface area22530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.425, 99.425, 156.698
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-517-

HOH

21A-581-

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-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG-400, HEPES 7.5, 0.2 M MgCl2 hexahydrate, 1mM Phenylalanine, 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: 2.45→41.5 Å / Num. all: 11346 / Num. obs: 11233 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15 % / Rsym value: 0.09 / Net I/σ(I): 14
Reflection shellResolution: 2.45→2.49 Å / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 8.2 / % 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 4PPU

4ppu


Resolution: 2.45→30.055 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 523 4.75 %RANDOM
Rwork0.1701 ---
obs0.1731 11004 98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.278 Å2 / ksol: 0.349 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3804 Å20 Å20 Å2
2--1.3804 Å2-0 Å2
3----2.7608 Å2
Refinement stepCycle: LAST / Resolution: 2.45→30.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 12 83 2077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112038
X-RAY DIFFRACTIONf_angle_d1.362752
X-RAY DIFFRACTIONf_dihedral_angle_d13.169776
X-RAY DIFFRACTIONf_chiral_restr0.077298
X-RAY DIFFRACTIONf_plane_restr0.008355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.69630.31181240.21542442X-RAY DIFFRACTION93
2.6963-3.08640.27031500.18922618X-RAY DIFFRACTION100
3.0864-3.88810.24191240.16942659X-RAY DIFFRACTION100
3.8881-30.0550.18881250.15082762X-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)
11.0537-0.0872-1.11090.08140.53023.7904-0.03730.04650.00830.03-0.04430.05210.0298-0.32030.08060.16140.03170.02090.17420.02870.188218.990331.74939.778
22.2597-0.8705-0.91931.08360.56533.06430.16840.04620.326-0.1340.0966-0.4085-0.40060.8776-0.22020.0765-0.08770.02820.28770.02830.192336.866942.8728-3.1859
33.7007-2.0163-2.32814.1883-0.0543.6180.1538-0.17480.3242-0.03290.0218-0.0384-0.44390.5542-0.18080.1843-0.0373-0.04430.2846-0.04340.090327.074345.179515.6315
40.60160.3139-0.98350.2456-1.04735.0225-0.1947-0.2638-0.13950.0413-0.1244-0.21390.23160.71540.19730.14090.1031-0.02750.37560.01560.255336.280430.8795.3373
50.60460.7162-1.52870.8452-1.83877.7279-0.2345-0.0726-0.1110.09020.0002-0.1221-0.0161-0.07760.09590.140.07330.00710.25640.01470.215527.420931.97810.9909
65.8450.15790.65753.5249-0.30580.30150.3096-0.0741-0.3761-0.0858-0.1988-0.25550.63780.6838-0.10380.37560.2299-0.01160.4230.13460.198732.787820.378229.2751
74.4818-0.19911.98026.9904-4.08953.5504-0.01150.0089-0.54740.1219-0.1084-0.53821.30420.15470.05010.47250.0650.0610.1653-0.05040.377421.740716.04415.7922
84.35590.97845.75784.41-1.04049.1360.07910.3654-0.5594-0.46450.13530.04231.11580.1876-0.20120.3560.06120.12060.2895-0.05210.332426.479818.5064-3.6372
92.4982-1.0561-2.8011.71541.33613.19450.1596-0.02460.0396-0.26-0.1756-0.4380.07580.76560.00920.21360.1451-0.00350.4050.07510.312232.593327.609823.5185
106.23344.2997-1.1523.9097-2.25142.46110.3607-0.65810.2710.38330.3328-0.06790.0744-0.0615-0.60170.16180.0772-0.00750.5256-0.0160.214820.330445.18612.1236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 79:111 )A79 - 111
2X-RAY DIFFRACTION2( CHAIN A AND RESID 112:148 )A112 - 148
3X-RAY DIFFRACTION3( CHAIN A AND RESID 149:178 )A149 - 178
4X-RAY DIFFRACTION4( CHAIN A AND RESID 179:211 )A179 - 211
5X-RAY DIFFRACTION5( CHAIN A AND RESID 212:243 )A212 - 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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