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- PDB-7etx: Crystal structure of bifunctional indole-3-glycerol phosphate syn... -

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Basic information

Entry
Database: PDB / ID: 7etx
TitleCrystal structure of bifunctional indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase (TrpC) from corynebacterium glutamicum
ComponentsTryptophan biosynthesis protein TrpCF
KeywordsBIOSYNTHETIC PROTEIN / Tryptophan biosynthesis / amino acid / bifunctional
Function / homology
Function and homology information


phosphoribosylanthranilate isomerase / indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / L-tryptophan biosynthetic process
Similarity search - Function
N-(5'phosphoribosyl) anthranilate isomerase (PRAI) domain / N-(5'phosphoribosyl)anthranilate (PRA) isomerase / Indole-3-glycerol phosphate synthase, conserved site / Indole-3-glycerol phosphate synthase signature. / Indole-3-glycerol phosphate synthase domain / Indole-3-glycerol phosphate synthase / Indole-3-glycerol phosphate synthase / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
Tryptophan biosynthesis protein TrpCF
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsPrak, W.J. / Kim, K.-J.
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Crystal Structure and Functional Characterization of the Bifunctional N -(5'-Phosphoribosyl)anthranilate Isomerase-indole-3-glycerol-phosphate Synthase from Corynebacterium glutamicum
Authors: Park, W. / Son, H.F. / Lee, D. / Kim, I.K. / Kim, K.J.
History
DepositionMay 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan biosynthesis protein TrpCF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7883
Polymers51,6041
Non-polymers1842
Water3,603200
1
A: Tryptophan biosynthesis protein TrpCF
hetero molecules

A: Tryptophan biosynthesis protein TrpCF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5776
Polymers103,2082
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5190 Å2
ΔGint-12 kcal/mol
Surface area36800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.681, 90.681, 141.785
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-796-

HOH

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Components

#1: Protein Tryptophan biosynthesis protein TrpCF


Mass: 51604.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: trpC, trpCF, Cgl3033, cg3362 / Production host: Escherichia coli (E. coli)
References: UniProt: P06560, indole-3-glycerol-phosphate synthase, phosphoribosylanthranilate isomerase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8M Pottasium sodium tartrate tetrahydrate, 0.1M Sodium HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 34548 / % possible obs: 98 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.024 / Rrim(I) all: 0.087 / Χ2: 3.16 / Net I/σ(I): 13.9 / Num. measured all: 352134
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.145.50.34516640.6320.1390.3761.4796.6
2.14-2.186.60.3416710.7040.1250.3651.5697.3
2.18-2.227.20.3217040.8090.1130.3411.68598.3
2.22-2.267.30.30616720.8650.1060.3261.74297.6
2.26-2.317.80.27817010.9190.0920.2951.82297.7
2.31-2.378.20.27316950.9230.0890.2891.98898.1
2.37-2.428.70.24616940.9510.0760.2582.17498
2.42-2.4990.22616780.9740.0690.2372.3797.2
2.49-2.569.30.20617070.9790.0620.2162.61297.6
2.56-2.6510.10.19116920.9850.0560.22.77797.6
2.65-2.7410.50.16717330.9910.0480.1742.99398.3
2.74-2.8510.80.15317220.9930.0440.163.20398.4
2.85-2.9811.60.12617120.9960.0350.1313.56497.9
2.98-3.1411.70.11117250.9960.0310.1153.77998.3
3.14-3.3312.30.09617440.9960.0270.13.96198.8
3.33-3.5912.60.08317590.9980.0230.0864.10499
3.59-3.9512.90.07517700.9980.020.0784.17699.4
3.95-4.5213.50.06718010.9980.0180.074.11799.4
4.52-5.714.30.06418160.9980.0170.0673.86799.5
5.7-5012.80.06118880.9980.0180.0633.74695.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→32.74 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.975 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1710 5 %RANDOM
Rwork0.1925 ---
obs0.1954 32811 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.21 Å2 / Biso mean: 46.552 Å2 / Biso min: 16.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å2-0 Å2-0 Å2
2--1.18 Å2-0 Å2
3----2.36 Å2
Refinement stepCycle: final / Resolution: 2.1→32.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3540 0 12 200 3752
Biso mean--64.13 47.17 -
Num. residues----472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133611
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173464
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.6274901
X-RAY DIFFRACTIONr_angle_other_deg1.2931.5767951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1175471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63121.568185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9615580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9261529
X-RAY DIFFRACTIONr_chiral_restr0.0660.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024147
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02803
LS refinement shellResolution: 2.101→2.156 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.341 107 -
Rwork0.366 2345 -
obs--96.12 %

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