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- PDB-6xin: The crystal structure of tryptophan synthase from Salmonella ente... -

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Basic information

Entry
Database: PDB / ID: 6xin
TitleThe crystal structure of tryptophan synthase from Salmonella enterica serovar typhimurium in complex with (2S)-3-Amino-3-imino-2-phenyldiazenylpropanamide at the enzyme alpha-site.
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / tryptophan synthase / alpha-chain / wild-type / recombinant protein / (2S)-3-Amino-3-imino-2-phenyldiazenylpropanamide
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / 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
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PYRIDOXAL-5'-PHOSPHATE / Chem-V41 / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsHilario, E. / Chang, C. / Mueller, L.J. / Dunn, M.F. / Fan, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-109045 United States
CitationJournal: To Be Published
Title: The crystal structure of tryptophan synthase from Salmonella enterica serovar typhimurium in complex with (2S)-3-Amino-3-imino-2-phenyldiazenylpropanamide at the enzyme alpha-site.
Authors: Hilario, E. / Chang, C. / Mueller, L.J. / Dunn, M.F. / Fan, L.
History
DepositionJun 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)75,95762
Polymers71,6182
Non-polymers4,33960
Water11,115617
1
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)151,914124
Polymers143,2354
Non-polymers8,678120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Unit cell
Length a, b, c (Å)182.300, 59.480, 67.165
Angle α, β, γ (deg.)90.000, 94.820, 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 (bacteria) / Gene: trpA, DD95_04145 / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: A0A0D6FWC1, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42918.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: trpB / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 9 types, 677 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#4: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#9: Chemical ChemComp-V41 / (2R,3Z)-3-amino-3-imino-2-[(E)-phenyldiazenyl]propanamide


Mass: 205.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11N5O / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-CS / CESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.58 Å3/Da / Density % sol: 52.33 % / Description: large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50 mM Bicine-CsOH, 8% PEG 8,000, 2 mM Spermine, pH 7.8, 50mM (2S)-3-Amino-3-imino-2-phenyldiazenylpropanamide
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: Aug 17, 2014 / 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: 1.746→90.828 Å / Num. all: 72343 / Num. obs: 72343 / % possible obs: 100 % / Redundancy: 4.2 % / Rpim(I) all: 0.071 / Rrim(I) all: 0.154 / Rsym value: 0.123 / Net I/av σ(I): 3.2 / Net I/σ(I): 9.6 / Num. measured all: 300525
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
1.75-1.843.90.4381.541114105360.2490.510.4382.2100
1.84-1.9640.2932.23973199290.1660.3470.2933.2100
1.96-2.094.10.212.93797593570.1170.2480.214.5100
2.09-2.264.10.1643.43546786960.090.1940.1646.4100
2.26-2.474.10.143.83265580540.0770.1650.147.9100
2.47-2.774.10.1274.22986672480.0710.1510.12710100
2.77-3.24.30.1224.42787064770.0710.1510.12214.1100
3.2-3.914.60.1154.52474954350.0680.1460.11522.8100
3.91-5.534.70.0985.12010342520.0560.1230.09829.3100
5.53-22.9784.70.0861099523590.0480.1050.0827.198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.546
Highest resolutionLowest resolution
Rotation22.98 Å1.92 Å

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Processing

Software
NameVersionClassification
MOSFLM7.3.0data reduction
SCALA3.3.21data scaling
MOLREP11.7.02phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HN4

4hn4


Resolution: 1.75→22.98 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.837 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 3637 5 %RANDOM
Rwork0.1646 ---
obs0.1666 68702 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.99 Å2 / Biso mean: 23.338 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20.01 Å2
2--0.26 Å20 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.75→22.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4935 0 226 633 5794
Biso mean--39.34 36.25 -
Num. residues----654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135348
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175089
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.6467199
X-RAY DIFFRACTIONr_angle_other_deg1.4881.57111769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7275683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49122.648253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53415859
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3661530
X-RAY DIFFRACTIONr_chiral_restr0.0920.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026013
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021057
LS refinement shellResolution: 1.75→1.791 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.296 236 -
Rwork0.276 4497 -
obs--89.15 %
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)
13.5044-0.46621.70060.0818-0.0294.16320.11950.05090.12420.0203-0.0247-0.00850.2478-0.267-0.09490.0946-0.00340.04590.09610.00710.0589-56.78638.7298-8.5157
21.37820.76280.09830.7023-0.14420.7214-0.04210.02590.0628-0.08270.0308-0.0237-0.2414-0.06760.01140.15190.0250.02130.026-0.01240.0526-42.959321.0331-12.6948
30.432-0.33720.15530.82190.2120.380.0424-0.0193-0.0001-0.0384-0.0307-0.0587-0.0405-0.01-0.01170.0386-0.00320.01190.0703-0.00390.0516-37.34668.4956-8.5055
41.7259-1.6489-0.41163.02960.08853.190.27080.1542-0.1776-0.0211-0.21290.14670.0082-0.1818-0.05790.08720.0108-0.04880.055-0.02150.0667-46.3486-4.0568-16.9387
50.63030.01630.72920.7758-0.12780.8898-0.03670.0638-0.0175-0.14040.03820.0663-0.06520.0446-0.00160.07360.0234-0.03370.0735-0.00340.023-48.705212.8242-22.5663
60.35010.0371-0.3080.28840.23780.67150.02760.0248-0.05810.0485-0.03920.01490.0421-0.17250.01160.0143-0.0141-0.01630.12690.01180.0588-27.9324-12.415-19.8626
70.39620.23870.13710.24020.29230.5466-0.06060.0834-0.0050.01310.05250.01270.09640.11150.00810.03570.0128-0.00270.1234-0.0130.0318-0.8566-17.1725-27.4235
80.0785-0.05420.14550.1114-0.05640.29660.02490.0139-0.0001-0.0291-0.0208-0.00770.03570.0111-0.00410.0275-0.0021-0.00230.1205-0.01160.0238-10.314-8.1989-30.3902
90.2617-0.538-0.08251.22620.80573.40080.0615-0.06550.0558-0.17540.1224-0.1481-0.3642-0.0934-0.18390.0756-0.01160.0750.0457-0.04840.1208-14.89177.9331-33.9696
100.1028-0.01810.09390.0046-0.01550.3785-0.0003-0.0169-0.0065-0.0002-0.01090.0020.0074-0.03970.01130.02850.0040.00410.1004-0.00630.0461-10.8233-9.5973-18.4107
112.03830.39650.29350.2960.27040.2506-0.0084-0.01330.29120.0086-0.0480.06580.0109-0.0460.05640.0110.01590.00410.0878-0.01230.1049-16.52043.0161-8.8588
120.56360.0999-0.10590.023-0.02920.318-0.0123-0.00390.039-0.00830.01920.0068-0.01440.0027-0.00690.0322-0.00090.00510.0960.00050.0430.5367-3.9711-13.1101
130.3175-0.29460.14450.4446-0.10880.69190.02730.03740.0103-0.02820.0315-0.031-0.12230.0589-0.05880.0518-0.01360.02210.10780.00190.01527.2114-0.0523-17.7168
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 14
2X-RAY DIFFRACTION2A15 - 42
3X-RAY DIFFRACTION3A43 - 159
4X-RAY DIFFRACTION4A160 - 179
5X-RAY DIFFRACTION5A190 - 268
6X-RAY DIFFRACTION6B2 - 37
7X-RAY DIFFRACTION7B38 - 70
8X-RAY DIFFRACTION8B71 - 126
9X-RAY DIFFRACTION9B127 - 165
10X-RAY DIFFRACTION10B166 - 269
11X-RAY DIFFRACTION11B270 - 301
12X-RAY DIFFRACTION12B302 - 364
13X-RAY DIFFRACTION13B365 - 397

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