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- PDB-7k0b: The internal aldimine form of Salmonella typhimurium Tryptophan S... -

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Basic information

Entry
Database: PDB / ID: 7k0b
TitleThe internal aldimine form of Salmonella typhimurium Tryptophan Synthase mutant beta-Q114A with cesium ion at the metal coordination site. A random beta-P270L mutation was inserted during PCR step
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / LYASE / inhibitor complex / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-tryptophan biosynthetic process / identical protein binding / cytoplasm / cytosol
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 / Pyridoxal-phosphate 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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / SERINE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 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)GM097569 United States
CitationJournal: To be Published
Title: The internal aldimine form of Salmonella typhimurium Tryptophan Synthase mutant beta-Q114A with cesium ion at the metal coordination site. A random beta-P270L mutation was inserted during PCR step.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionSep 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 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)74,62941
Polymers71,5772
Non-polymers3,05239
Water12,196677
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 area9540 Å2
ΔGint-109 kcal/mol
Surface area24270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.939, 58.379, 67.199
Angle α, β, γ (deg.)90.000, 94.630, 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: 42877.871 Da / Num. of mol.: 1 / Mutation: Q114A, P270L
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): beta-Q114A, beta-P270L / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 10 types, 716 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#11: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / 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: 51.84 % / Description: Plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 50 mM Bicine-CsOH, 9% PEG 8,000, 4 mM Spermine / PH range: 7.6-8.0 / Temp details: constante

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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: Apr 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.57→91.171 Å / Num. obs: 97213 / % possible obs: 98.6 % / Redundancy: 4.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.047 / Rrim(I) all: 0.103 / Rsym value: 0.077 / Net I/av σ(I): 4.3 / Net I/σ(I): 9
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
1.57-1.654.70.6281.265987141900.3770.8240.628299.1
1.65-1.764.70.4161.763505134780.2530.5490.416399.3
1.76-1.884.80.282.561229126680.170.370.284.499.3
1.88-2.034.50.1893.652971117640.120.2540.1896.299
2.03-2.224.90.1175.652668108250.0710.1560.1179.598.9
2.22-2.484.60.0887.14515997340.0560.120.0881298.2
2.48-2.874.60.078.33924185540.0440.0960.0714.997.9
2.87-3.514.70.068.23396472190.0360.080.0618.997
3.51-4.964.60.0559.22586856180.0320.0720.05522.597.2
4.96-39.1854.60.067.81447231630.0360.0780.0622.697.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.54
Highest resolutionLowest resolution
Rotation39.19 Å1.73 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 97136
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.51-10037.30.909649
6.02-8.5146.10.8881130
4.91-6.0240.30.8891482
4.26-4.9129.40.9321722
3.81-4.2628.50.911947
3.47-3.8128.10.9112121
3.22-3.47290.9052290
3.01-3.2228.90.8872479
2.84-3.0129.60.8752660
2.69-2.8427.70.8822772
2.57-2.6927.40.8832972
2.46-2.57280.8693079
2.36-2.4626.70.8733237
2.27-2.3624.70.8743340
2.2-2.2725.70.8643481
2.13-2.224.40.8743562
2.06-2.1324.40.8773725
2.01-2.0626.60.8663845
1.95-2.0125.80.8623912
1.9-1.9525.30.8534076
1.86-1.925.80.8434117
1.81-1.8626.30.8444260
1.77-1.8127.10.8284353
1.74-1.7727.50.7964477
1.7-1.7428.50.7874568
1.67-1.7290.7544594
1.64-1.6731.70.7274737
1.61-1.6433.80.7044801
1.57-1.6141.80.5956748

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Processing

Software
NameVersionClassification
XDSJun 1, 2017 BUILT=20170923data reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
DM7.1.003phasing
REFMAC5.8.0266refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6X0C

6x0c


Resolution: 1.57→39.18 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.92 / SU ML: 0.099 / SU R Cruickshank DPI: 0.0927 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 4889 5 %RANDOM
Rwork0.199 ---
obs0.2009 92248 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.69 Å2 / Biso mean: 29.468 Å2 / Biso min: 15.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0 Å20.07 Å2
2--0.07 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.57→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4906 0 158 692 5756
Biso mean--51.01 41.69 -
Num. residues----651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125178
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.6346980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4875660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03122.191251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77915832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4291533
X-RAY DIFFRACTIONr_chiral_restr0.1070.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023943
LS refinement shellResolution: 1.57→1.611 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 357 -
Rwork0.391 6822 -
all-7179 -
obs--98.99 %
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)
16.36250.22540.63020.01110.13195.79130.1344-0.028-0.13120.0036-0.00190.00010.22310.4604-0.13250.08550.00420.00180.1362-0.01040.130257.09627.60377.8016
20.10090.11530.34370.13380.38031.33560.0126-0.01260.00870.0129-0.00880.0251-0.14270.035-0.00380.1387-0.05370.03750.0966-0.01240.15142.645216.956414.0351
30.46180.4226-0.04110.4744-0.07890.30260.0579-0.0042-0.0012-0.0212-0.04540.0172-0.03280.0192-0.01250.1064-0.00180.01850.1196-0.00070.123637.59277.45157.7276
40.74970.07150.79732.3161.26921.49010.1478-0.118-0.17390.07610.0579-0.10760.133-0.0526-0.20570.0837-0.0523-0.0450.18990.02670.121749.4684-2.824919.9011
52.8956-1.97270.9572.1854-0.12960.6940.036-0.1099-0.11490.1158-0.00440.0824-0.0023-0.0157-0.03160.1784-0.11590.0190.2141-0.02510.00946.444316.182724.2657
64.2653-3.57352.56646.2354-2.02471.6469-0.3-0.00150.3020.65350.0593-0.1898-0.31440.1260.24080.2505-0.1608-0.05970.17420.02880.038850.375223.695120.9159
70.83820.0503-0.36720.0577-0.12570.39750.01640.0239-0.0523-0.0274-0.0395-0.00730.05980.14990.02310.07230.0182-0.01390.1791-0.00010.108127.7698-12.976519.483
80.4084-0.1216-0.20630.1335-0.15130.5736-0.1097-0.0311-0.0240.02390.0395-0.02350.0828-0.07640.07020.0908-0.0062-0.01250.1393-0.00250.10941.1867-17.578527.7396
90.07250.04020.01970.03550.09470.57220.0431-0.03660.01620.0177-0.02040.01140.00870.0177-0.02270.09740.0034-0.00940.14130.00780.116710.4216-8.630330.288
100.5481-0.01850.21990.8596-0.55821.79260.1404-0.09920.18440.0887-0.0144-0.0344-0.19290.0235-0.1260.1088-0.02410.04980.1067-0.00410.138614.37817.262332.4069
110.19420.0009-0.13840.03570.06010.2360.01020.02190.01340.01140.00020.0050.04230.0483-0.01040.09450.0021-0.00730.16160.01010.10912.837-11.332421.2834
120.52330.1309-0.33980.0339-0.08570.22430.01840.11150.06290.00660.02190.0055-0.0061-0.0509-0.04030.0773-0.00330.00880.17060.01770.138512.6546-0.65648.1713
130.8422-0.1884-0.19460.05820.12510.4834-0.010.03080.06770.00280.0078-0.0121-0.0133-0.0040.00220.0899-0.00260.00760.15080.01740.10850.2608-3.154413.2646
140.25680.18560.15280.60550.63241.10380.05880.0260.01930.0180.023-0.0217-0.097-0.1036-0.08180.10190.01770.03180.16560.02510.0763-7.1358-0.983217.8019
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 13
2X-RAY DIFFRACTION2A14 - 61
3X-RAY DIFFRACTION3A62 - 159
4X-RAY DIFFRACTION4A160 - 216
5X-RAY DIFFRACTION5A217 - 247
6X-RAY DIFFRACTION6A248 - 268
7X-RAY DIFFRACTION7B2 - 37
8X-RAY DIFFRACTION8B38 - 70
9X-RAY DIFFRACTION9B71 - 126
10X-RAY DIFFRACTION10B127 - 165
11X-RAY DIFFRACTION11B166 - 244
12X-RAY DIFFRACTION12B245 - 295
13X-RAY DIFFRACTION13B296 - 364
14X-RAY DIFFRACTION14B365 - 396

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