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- PDB-7jqw: The external aldimine crystal structure of Salmonella typhimurium... -

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Entry
Database: PDB / ID: 7jqw
TitleThe external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex with cesium ion at the metal coordination site. The single beta-Q114 rotamer conformation allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring
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
2-AMINOPHENOL / : / Chem-KOU / SERINE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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 external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex with cesium ion at the metal coordination site. The single beta-Q114 rotamer ...Title: The external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A in complex with cesium ion at the metal coordination site. The single beta-Q114 rotamer conformation allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionAug 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 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)74,41939
Polymers71,6022
Non-polymers2,81737
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-143 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.714, 58.653, 67.030
Angle α, β, γ (deg.)90.000, 94.980, 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: 42902.879 Da / Num. of mol.: 1 / Mutation: S377A
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): S377A / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 8 types, 441 molecules

#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-2AF / 2-AMINOPHENOL


Mass: 109.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H7NO
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-KOU / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine


Mass: 334.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#9: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.56 Å3/Da / Density % sol: 52.04 % / Description: Large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM Bicine-CsOH, 10% PEG 8,000, 4 mM Spermine, pH 8.0
PH range: 7.6-8.0 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cobra System / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 16, 2020 / Details: Osmic Varimax HF ArcSec
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→91.012 Å / Num. obs: 73477 / % possible obs: 94.6 % / Redundancy: 2.7 % / Rpim(I) all: 0.068 / Rrim(I) all: 0.118 / Rsym value: 0.084 / Net I/av σ(I): 2.9 / Net I/σ(I): 4.2
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
1.75-1.842.70.329127451101700.2380.4110.3292.798.4
1.84-1.962.60.2451.52498494440.1790.3060.2453.196.4
1.96-2.092.60.1981.42314887580.1450.2460.1983.695.4
2.09-2.262.70.1611.32108479340.1150.1960.1614.292.6
2.26-2.472.70.1272.81903271360.0930.1580.1274.690.5
2.47-2.772.70.1143.21782065040.0840.1450.114590.8
2.77-3.22.80.122.31669459410.0860.1520.125.493.7
3.2-3.912.90.083.61496251380.0590.1050.085.896
3.91-5.5330.0387.51190440120.0330.0580.038696
5.53-39.22230.0348.8661522390.0330.060.034696

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.4
Highest resolutionLowest resolution
Rotation39.22 Å1.84 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 73477
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.22-10029.90.919508
6.52-9.2234.60.908896
5.32-6.5233.40.91111
4.61-5.3223.50.941321
4.12-4.6120.40.9371524
3.76-4.1222.50.9271685
3.48-3.7618.80.9451821
3.26-3.4819.10.9481923
3.07-3.2618.50.9492018
2.91-3.0719.50.9422131
2.78-2.91190.9442212
2.66-2.7818.60.9482283
2.56-2.6618.30.9472328
2.46-2.5618.30.952431
2.38-2.4618.80.9452506
2.3-2.3819.50.9392635
2.24-2.319.10.9392667
2.17-2.2419.30.9382818
2.11-2.1720.10.9412917
2.06-2.1120.70.9333068
2.01-2.0621.20.9313121
1.96-2.01220.9343224
1.92-1.96230.9333295
1.88-1.92260.9233401
1.84-1.8829.20.9173506
1.81-1.8430.60.9113618
1.77-1.8132.90.9123676
1.74-1.7734.20.8973739
1.7-1.7440.10.8735094

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Processing

Software
NameVersionClassification
xia20.6.0data reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
DM7.1.002phasing
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6X0C

6x0c


Resolution: 1.7→39.22 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2303 3641 4.96 %
Rwork0.1936 69762 -
obs0.1954 73403 94.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.97 Å2 / Biso mean: 25.1768 Å2 / Biso min: 2.35 Å2
Refinement stepCycle: final / Resolution: 1.7→39.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4875 0 136 422 5433
Biso mean--39.59 38.53 -
Num. residues----648
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.720.29831290.2981261190
1.72-1.750.35041340.2992273698
1.75-1.770.31011440.2763279698
1.77-1.80.27951400.266273898
1.8-1.830.31091660.2687276398
1.83-1.860.30071320.2632279598
1.86-1.890.29491440.2554273197
1.89-1.920.32531400.238272695
1.92-1.960.27931380.2302270696
1.96-20.231540.2125266796
2-2.040.24291530.2052269395
2.04-2.090.24661320.1992272295
2.09-2.140.24181320.1941257392
2.14-2.20.22051290.1876265593
2.2-2.260.24021250.1853259391
2.26-2.340.21071420.1898260591
2.34-2.420.22441510.1834251090
2.42-2.520.2191500.1869253189
2.52-2.630.20091310.1857258190
2.63-2.770.22161650.1757256891
2.77-2.950.22421240.1789268193
2.95-3.170.20471380.1688267894
3.17-3.490.21881400.1611270595
3.49-40.18781530.1509278097
4-5.030.18111260.1527279496
5.03-39.220.24091290.2147282495
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)
10.03530.03730.02010.03210.01320.0782-0.08370.10280.12930.00490.1111-0.1196-0.25720.21840.00010.1818-0.0404-0.00080.2484-0.0050.262549.71615.16211.141
20.012-0.00840.00370.07550.03970.0637-0.1355-0.11250.05660.17620.0140.0415-0.1485-0.0483-0.00010.1897-0.03050.030.1902-0.00680.220535.89515.74310.633
30.0707-0.01710.01240.1104-0.01780.01380.07790.0488-0.0429-0.0235-0.0847-0.03210.00650.0397-0.01520.0936-0.0420.02630.13270.00770.127139.0222.1316.906
40.0077-0.00950.00290.0119-0.01060.00890.0767-0.0179-0.21820.03480.0621-0.11640.13220.15010.00140.19340.0076-0.07530.19090.01750.367649.195-5.49318.6
50.0060.00040.00690.0219-0.01920.02180.094-0.0822-0.10780.2872-0.0672-0.0544-0.09050.03220.00070.2134-0.0458-0.04010.2637-0.02510.220552.0346.54522.994
60.01160.0204-0.00120.028-0.02140.01-0.0458-0.19580.09560.1363-0.1351-0.0026-0.40770.1075-0.00290.31340.0297-0.02540.2141-0.04550.235346.15623.87721.164
70.04520.04170.04270.0880.02550.1946-0.134-0.0033-0.2557-0.08750.0378-0.12950.11520.4264-0.02670.06560.0246-0.00820.18560.02460.127327.68-13.13919.585
80.3748-0.0693-0.46480.12270.02440.61740.1154-0.06550.06470.0027-0.0582-0.0385-0.06030.06340.08840.0533-0.0231-0.00090.00940.02420.04418.906-6.02530.203
90.12350.00290.17330.20870.13340.35850.3676-0.07470.2028-0.1151-0.0101-0.2176-0.22830.09490.14130.0808-0.06440.060.18070.01920.164224.204-1.86725.893
100.2721-0.1621-0.11080.15820.05260.2880.09970.3132-0.0076-0.0813-0.1916-0.05630.10010.4429-0.08910.09350.03210.0083-0.43070.0510.04655.06-13.30115.096
110.0554-0.03040.05190.0127-0.04290.06550.00740.0520.27720.02480.0216-0.0009-0.09050.03250.01730.0967-0.03780.00070.11820.03690.191616.733.1819.314
120.06560.050.01970.0294-0.03940.1680.0570.08370.072-0.0087-0.0268-0.0193-0.076-0.04210.03230.08370.0069-0.00370.0610.01010.06242.372-4.15612.384
130.0990.08630.02750.0634-0.03610.14320.08930.02050.04490.0042-0.0063-0.0392-0.0815-0.13890.02670.09510.00820.01370.07570.00750.0579-6.795-2.13116.317
142.19812.6219-2.86835.7946-5.77796.1165-0.10012.12170.05930.5415-0.3656-0.3399-0.5173-0.4570.46950.825-0.07740.01730.7802-0.17080.853216.3365.7342.151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:42 )A1 - 42
2X-RAY DIFFRACTION2( CHAIN A AND RESID 43:91 )A43 - 91
3X-RAY DIFFRACTION3( CHAIN A AND RESID 92:159 )A92 - 159
4X-RAY DIFFRACTION4( CHAIN A AND RESID 160:202 )A160 - 202
5X-RAY DIFFRACTION5( CHAIN A AND RESID 203:234 )A203 - 234
6X-RAY DIFFRACTION6( CHAIN A AND RESID 235:268 )A235 - 268
7X-RAY DIFFRACTION7( CHAIN B AND RESID 2:37 )B2 - 37
8X-RAY DIFFRACTION8( CHAIN B AND RESID 38:165 )B38 - 165
9X-RAY DIFFRACTION9( CHAIN B AND RESID 166:196 )B166 - 196
10X-RAY DIFFRACTION10( CHAIN B AND RESID 197:269 )B197 - 269
11X-RAY DIFFRACTION11( CHAIN B AND RESID 270:301 )B270 - 301
12X-RAY DIFFRACTION12( CHAIN B AND RESID 302:343 )B302 - 343
13X-RAY DIFFRACTION13( CHAIN B AND RESID 344:396 )B344 - 396
14X-RAY DIFFRACTION14( CHAIN B AND RESID 417:417 )B417

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