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- PDB-7kh6: 1.45 Angstrom resolution internal aldimine crystal structure of t... -

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Entry
Database: PDB / ID: 7kh6
Title1.45 Angstrom resolution internal aldimine crystal structure of the beta-Q114A mutant of TryptophanSynthase in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / inhibitor / LYASE / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme ...Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / Chem-F9F / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsHilario, E. / Dunn, M.F. / Mueller, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)2R01GM097569-06A1 United States
CitationJournal: To be Published
Title: 1.45 Angstrom resolution internal aldimine crystal structure of the beta-Q114A mutant of Tryptophan Synthase in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate ...Title: 1.45 Angstrom resolution internal aldimine crystal structure of the beta-Q114A mutant of Tryptophan Synthase in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionOct 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,04828
Polymers71,5612
Non-polymers2,48826
Water14,610811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Tryptophan Synthase complex (alpha2-beta2) Protein is a tetramer in solution and composed of two alpha-chains and two beta-chains.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-98 kcal/mol
Surface area24280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.516, 58.931, 67.555
Angle α, β, γ (deg.)90.000, 94.880, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Tryptophan synthase ... , 2 types, 2 molecules AB

#1: Protein Tryptophan synthase alpha chain


Mass: 28698.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpA, STM1727 / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42861.828 Da / Num. of mol.: 1 / Mutation: Q114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpB, STM1726 / Plasmid: pEBA-10 / Details (production host): Q114A / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 8 types, 837 molecules

#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-F9F / 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE / N-(4'-TRIFLUOROMETHOXYBENZENESULFONYL)-2-AMINO-1-ETHYLPHOSPHATE, F9


Mass: 365.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11F3NO7PS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 811 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.79 % / Description: Large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 50 mM Bicine-CsOH, 9% PEG 8,000, 4 mM Spermine / PH range: 7.6-8.0 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.45→90.927 Å / Num. obs: 126467 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.061 / Rrim(I) all: 0.167 / Rsym value: 0.14 / Net I/av σ(I): 2.7 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.45-1.536.50.8790.7118698183840.3961.0390.8791.799.9
1.53-1.626.80.5731.1118677174190.2460.6670.5732.699.9
1.62-1.736.80.4041.5111723164100.1750.4730.4043.7100
1.73-1.876.80.2742.2104288152280.1190.3230.2745.199.9
1.87-2.056.90.2192.396971140140.0980.2640.2196.8100
2.05-2.297.30.1682.993084127290.0740.2030.1688.8100
2.29-2.656.90.1274.678017112480.0560.1520.1279.7100
2.65-3.247.60.1194.27229895060.0510.1430.11911.399.9
3.24-4.596.90.0985.15142774040.0430.1170.09811.999.9
4.59-36.7837.30.0785.93030041250.0320.090.07812.399.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.28 Å36.78 Å
Translation7.28 Å36.78 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 126456
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.86-10035.90.899852
5.56-7.8640.80.8761485
4.54-5.5627.20.9291904
3.93-4.5423.30.9412276
3.51-3.9324.60.9312559
3.21-3.5123.70.9292808
2.97-3.2123.50.9333060
2.78-2.9724.60.9253282
2.62-2.7823.10.933509
2.49-2.6222.60.9263691
2.37-2.4922.50.933873
2.27-2.3721.50.9294010
2.18-2.2720.90.9234216
2.1-2.1821.20.9274397
2.03-2.1230.8834529
1.96-2.0322.60.9214700
1.91-1.9622.60.8974814
1.85-1.9123.60.9085010
1.8-1.8522.50.9225136
1.76-1.822.80.9275225
1.71-1.7622.90.9235354
1.68-1.71230.9255525
1.64-1.6825.90.925608
1.6-1.6426.70.9245762
1.57-1.627.60.9235869
1.54-1.5730.30.9126001
1.51-1.5431.30.8866111
1.49-1.5136.20.9026239
1.45-1.4941.50.8528651

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Processing

Software
NameVersionClassification
iMOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.6.1phasing
DM7.0.078phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C73

6c73


Resolution: 1.45→36.81 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.577 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0731 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 6421 5.1 %RANDOM
Rwork0.1583 ---
obs0.1605 120035 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.21 Å2 / Biso mean: 23.006 Å2 / Biso min: 7.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å2-0.23 Å2
2---1.03 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.45→36.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4988 0 119 850 5957
Biso mean--35.78 41.69 -
Num. residues----662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125504
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.6327476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9745726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41722.127268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03715899
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7691536
X-RAY DIFFRACTIONr_chiral_restr0.0970.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024278
X-RAY DIFFRACTIONr_rigid_bond_restr2.04535503
LS refinement shellResolution: 1.45→1.487 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 464 -
Rwork0.287 8723 -
all-9187 -
obs--98.67 %
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)
10.00030.0001-0.00070.0001-0.00030.0021-0.0003-0.0003-0.001-0.00010.0002-0.0004-0-0.00030.00010.000300.00170.01810.00010.0137.92399.97738.9064
20.0773-0.0297-0.03760.05180.01360.0183-0.0076-0.00340.00140.00410.0078-0.00030.00380.0013-0.00020.00140.0010.00210.0183-0.00070.008646.9679-1.653721.9417
30.0169-0.08080.01160.3904-0.05530.0080.00250.00330.0063-0.0057-0.0078-0.02820.0010.0030.00540.00470.00120.00530.01990.00260.009347.896316.363122.3802
40.0026-0.0026-00.0026-00.00010.000600.0002-0.000400.0008-0.00020.0009-0.00070.0008-0.00040.00260.0166-0.00050.01112.2766-14.270224.8211
50.0226-0.02720.01790.0343-0.02270.0151-0.0012-0.001-0.00180.00050.0003-0.0015-0.0002-0.00030.00090.0012-0.00050.00140.0172-0.00140.009515.04933.134233.0888
60.0058-0.00360.00420.0023-0.00270.0031-0.00090.0001-0.0010.00040.0009-0.0002-0.0006-0.00100.00070.00010.00260.0164-0.00020.010812.6941-11.342421.2887
70.00760.00760.00570.00790.00610.0047-0.0005-0.0012-0.0025-0.00060.0002-0.0008-0.0005-0.00040.00030.0011-0.00010.0020.0172-0.00020.010211.77830.03569.029
80.0118-0.0031-0.01530.01110.00850.0224-0.0011-0.0005-0.00220.0001-0.00040.00090.0017-0.00140.00150.0005-0.00050.00130.0163-0.00010.00982.3312-4.269212.5975
900000000000000-00.0063000.006300.0063000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 159
2X-RAY DIFFRACTION2A160 - 202
3X-RAY DIFFRACTION3A203 - 268
4X-RAY DIFFRACTION4B2 - 100
5X-RAY DIFFRACTION5B101 - 165
6X-RAY DIFFRACTION6B166 - 244
7X-RAY DIFFRACTION7B245 - 301
8X-RAY DIFFRACTION8B302 - 343
9X-RAY DIFFRACTION9B344 - 295

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