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

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Basic information

Entry
Database: PDB / ID: 7ety
TitleCrystal structure of bifunctional indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase (trpC) from Corynebacterium glutamicum in complex with reduced 1-(O-carboxyphenylamino)-1-deoxyribulose 5-phosphate (rCdRP)
ComponentsTryptophan biosynthesis protein TrpCF
KeywordsBIOSYNTHETIC PROTEIN / Tryptophan biosynthesis / amino acid / bifunctional
Function / homology
Function and homology information


phosphoribosylanthranilate isomerase / L-tryptophan metabolic process / 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
Chem-137 / Tryptophan biosynthesis protein TrpCF
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.21 Å
AuthorsPark, 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 1.1Nov 13, 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
B: Tryptophan biosynthesis protein TrpCF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,71818
Polymers103,2082
Non-polymers2,51016
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9930 Å2
ΔGint-15 kcal/mol
Surface area32940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.740, 98.163, 116.124
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tryptophan biosynthesis protein TrpCF


Mass: 51604.117 Da / Num. of mol.: 2
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-137 / 1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-PHOSPHATE


Mass: 351.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H18NO9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 22% (v/v) PEG 3350, 0.2M Magnesium chloride hexahydrate

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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: Apr 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 51884 / % possible obs: 99.1 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.042 / Rrim(I) all: 0.104 / Χ2: 2.746 / Net I/σ(I): 12.3 / Num. measured all: 286005
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.244.70.28925400.8760.1410.3231.64998.7
2.24-2.284.70.27625600.8840.1350.3081.7198.8
2.28-2.324.80.25125570.9070.1210.281.71898.8
2.32-2.374.80.24125430.9160.1160.2691.83398.6
2.37-2.424.80.22525290.9340.1070.251.81798.5
2.42-2.484.90.20425530.9470.0970.2271.84998.8
2.48-2.5450.19625300.9550.0910.2172.03298.5
2.54-2.615.10.18225640.960.0840.2012.19698.9
2.61-2.695.10.16625790.9710.0760.1832.23999.3
2.69-2.775.20.14925730.9770.0680.1642.34499.2
2.77-2.875.30.13725820.9830.0620.1512.39498.8
2.87-2.995.50.1225940.9860.0530.1322.54999.2
2.99-3.125.70.10925690.9860.0480.1192.80299.5
3.12-3.2960.09926110.990.0430.1082.93299.6
3.29-3.496.30.0926240.9930.0370.0973.36899.7
3.49-3.766.50.08126270.9940.0330.0883.81999.7
3.76-4.146.60.0726260.9960.0290.0763.90399.8
4.14-4.746.50.06626530.9950.0270.0724.19899.5
4.74-5.976.40.06226680.9960.0260.0673.33199.6
5.97-5060.05728020.9970.0250.0633.62598.7

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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: 2.21→34.61 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.736 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 2538 4.9 %RANDOM
Rwork0.1515 ---
obs0.1543 49311 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.38 Å2 / Biso mean: 27.097 Å2 / Biso min: 7.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--1.33 Å2-0 Å2
3----1.17 Å2
Refinement stepCycle: final / Resolution: 2.21→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6987 0 164 463 7614
Biso mean--42.96 31.46 -
Num. residues----931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137270
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176967
X-RAY DIFFRACTIONr_angle_refined_deg1.581.6299856
X-RAY DIFFRACTIONr_angle_other_deg1.3361.57615998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5621.397365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.415151152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0171559
X-RAY DIFFRACTIONr_chiral_restr0.0710.2957
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028236
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021606
LS refinement shellResolution: 2.21→2.24 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.262 174 -
Rwork0.192 3501 -
obs--96.36 %

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