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- PDB-7k5a: The external aldimine form of Salmonella typhimurium Tryptophan S... -

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Basic information

Entry
Database: PDB / ID: 7k5a
TitleThe external aldimine form of Salmonella typhimurium Tryptophan Synthase mutant beta-Q114A in complex with cesium ion at the metal coordination site.
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / tryptophan synthase
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
: / Chem-KOU / DI(HYDROXYETHYL)ETHER / 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: 1.5 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 form of Salmonella typhimurium Tryptophan Synthase mutant beta-Q114A in complex with cesium ion at the metal coordination site.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J.
History
DepositionSep 16, 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)73,18520
Polymers71,5612
Non-polymers1,62418
Water11,638646
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 area5210 Å2
ΔGint-102 kcal/mol
Surface area23890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.827, 59.527, 67.478
Angle α, β, γ (deg.)90.000, 94.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-845-

HOH

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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): strain 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): beta-Q114A / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 8 types, 664 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: 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
#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.: 646 / 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: 2.61 Å3/Da / Density % sol: 52.99 % / Description: large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50 mM Bicine-CsOH, 9% PEG 8,000, 3 mM Spermine, pH 7.8
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: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.5→91.082 Å / Num. obs: 113436 / % possible obs: 98.2 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.037 / Rrim(I) all: 0.095 / Rsym value: 0.082 / Net I/av σ(I): 4.2 / Net I/σ(I): 9.2
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
1.5-1.586.60.7151109606166410.3240.8350.715299.3
1.58-1.686.30.4831.599246157640.2240.5670.4832.899.1
1.68-1.796.70.2982.499150148670.1330.3460.2984.399.4
1.79-1.946.60.2113.391299137670.0940.2430.2116.298.9
1.94-2.126.20.1364.978035125640.0630.1580.1368.998
2.12-2.376.30.0996.271742113300.0450.1140.09912.597.3
2.37-2.746.30.0777.86294599330.0350.090.07715.596.7
2.74-3.3560.0678.54974582980.030.0770.0671995.4
3.35-4.746.50.0599.34289865640.0260.0680.05925.197.1
4.74-39.296.40.0618.12356537080.0270.070.06124.797.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.45 Å39.29 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 113150
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.13-10033.50.915770
5.75-8.1339.50.8971355
4.69-5.7531.20.9021702
4.07-4.6922.60.9442031
3.64-4.0722.30.9272265
3.32-3.6422.30.9242470
3.07-3.3223.30.9132682
2.87-3.0724.70.9132829
2.71-2.8723.90.9123030
2.57-2.7123.10.9133252
2.45-2.5723.90.9083397
2.35-2.4523.40.9123587
2.26-2.3522.20.9133763
2.17-2.2621.40.9133844
2.1-2.1722.50.9124014
2.03-2.124.20.9024219
1.97-2.0324.30.94339
1.92-1.9724.70.8864401
1.87-1.9224.90.8844610
1.82-1.8726.10.8934717
1.77-1.8226.70.8934878
1.73-1.7727.80.8844993
1.7-1.73280.895078
1.66-1.7320.8635199
1.63-1.6633.30.8585313
1.59-1.6333.50.8695386
1.56-1.5935.30.8625475
1.54-1.5638.10.8565644
1.5-1.5443.80.8087907

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Processing

Software
NameVersionClassification
XDSVERSION Jun 1, 2017 BUILT=20170923)data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
DM7.1.003phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7k0b

7k0b


Resolution: 1.5→39.29 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.166 / SU ML: 0.066 / SU R Cruickshank DPI: 0.0832 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22 5713 5 %RANDOM
Rwork0.1683 ---
obs0.1709 107437 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.61 Å2 / Biso mean: 30.771 Å2 / Biso min: 12.52 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å2-0 Å20.46 Å2
2--1.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 1.5→39.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4897 0 80 656 5633
Biso mean--43.12 41.73 -
Num. residues----650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125190
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.6337033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2235674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5322.283254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8215849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9981533
X-RAY DIFFRACTIONr_chiral_restr0.1010.2675
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023978
X-RAY DIFFRACTIONr_rigid_bond_restr4.10835190
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 440 -
Rwork0.281 7936 -
all-8376 -
obs--99.01 %
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)
10.04870.002-0.0830.83340.81740.95130.1073-0.06510.07570.2142-0.07170.07620.03510.0429-0.03560.2599-0.16430.15250.1297-0.04770.226341.504717.83313.6003
20.96510.8821-0.24171.0077-0.24850.06670.1415-0.01890.07730.0356-0.11140.046-0.02930.0269-0.03020.0897-0.00160.04150.12320.00830.158437.31097.73777.5286
31.9032-0.91860.8220.7113-0.69341.98240.0693-0.2046-0.0955-0.002-0.0637-0.1604-0.00840.2078-0.00560.0171-0.0379-0.03590.20180.09320.213249.0536-4.880119.3915
40.5728-0.2330.17960.6452-0.40910.27820.0491-0.10820.03310.1629-0.05360.0338-0.10350.06020.00450.0755-0.0391-0.02010.1416-0.03630.144248.031716.453322.3273
50.64250.0485-0.59690.0072-0.05870.7166-0.0282-0.0467-0.1175-0.0113-0.0253-0.010.01230.18870.05350.06550.0047-0.00780.16850.01380.140927.6307-12.74719.7296
60.18690.001-0.20370.0739-0.11870.4254-0.0637-0.0444-0.0221-0.00590.0328-0.01840.0747-0.04920.03090.09560.00370.0010.130.01260.13221.1788-17.38527.8782
70.0414-0.0113-0.1410.00820.06490.6950.0364-0.0405-0.0227-0.0063-0.0062-0-0.08610.093-0.03010.1069-0.01620.00350.13920.00890.123212.8478-5.21227.9462
80.4526-0.27020.08860.1757-0.0770.0806-0.01160.07370.11090.0075-0.0303-0.05330.01950.01140.04180.0886-0.00270.01050.12010.02310.150811.88290.28958.7809
90.3509-0.1823-0.0720.15880.08570.359-0.00750.04580.02820.0160.0064-0.0139-0.0184-0.00760.00120.09810.00590.01030.11340.00750.12772.4114-3.92312.4364
100.1330.0728-0.03530.04160.00470.55450.04420.02210.00410.02430.01670.0039-0.0794-0.0703-0.06090.11090.01310.01840.14290.00330.1139-6.4431-2.478216.41
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 61
2X-RAY DIFFRACTION2A62 - 159
3X-RAY DIFFRACTION3A160 - 202
4X-RAY DIFFRACTION4A203 - 268
5X-RAY DIFFRACTION5B2 - 37
6X-RAY DIFFRACTION6B38 - 70
7X-RAY DIFFRACTION7B71 - 224
8X-RAY DIFFRACTION8B245 - 301
9X-RAY DIFFRACTION9B302 - 343
10X-RAY DIFFRACTION10B344 - 395

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