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- PDB-4wx2: Crystal structure of Tryptophan Synthase from Salmonella typhimur... -

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Basic information

Entry
Database: PDB / ID: 4wx2
TitleCrystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with two F6F molecules in the alpha-site and one F6F molecule in the beta-site
Components(Tryptophan synthase ...) x 2
KeywordsTRANSFERASE / carbon-oxygen lyase / tryptophan biosynthesis / Salmonella typhimurium / F6F / inhibitor / allosteric enzyme / aromatic amino acid biosynthesis / pyridoxal phosphate
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. / Rossmann fold - #1100 / 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. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-F6F / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsHilario, E. / Caulkins, B.G. / Young, R.P. / Niks, D. / Dunn, M.F. / Mueller, L.J. / Fan, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM097569 United States
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Visualizing the tunnel in tryptophan synthase with crystallography: Insights into a selective filter for accommodating indole and rejecting water.
Authors: Hilario, E. / Caulkins, B.G. / Huang, Y.M. / You, W. / Chang, C.E. / Mueller, L.J. / Dunn, M.F. / Fan, L.
History
DepositionNov 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)73,0439
Polymers71,6182
Non-polymers1,4267
Water10,881604
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)146,08718
Polymers143,2354
Non-polymers2,85214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area14550 Å2
ΔGint-20 kcal/mol
Surface area42860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.809, 58.890, 67.270
Angle α, β, γ (deg.)90.000, 95.210, 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 enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: trpA / Plasmid: Derivative of Pbr322 / Production host: Escherichia coli (E. coli) / Strain (production host): Cb149 / References: UniProt: P00929, 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: Derivative of Pbr322 / Production host: Escherichia coli (E. coli) / Strain (production host): Cb149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 6 types, 611 molecules

#3: Chemical ChemComp-F6F / 2-{[4-(TRIFLUOROMETHOXY)BENZOYL]AMINO}ETHYL DIHYDROGEN PHOSPHATE / N-(4'-TRIFLUOROMETHOXYBENZOYL)-2-AMINO-1-ETHYLPHOSPHATE, F6


Mass: 329.166 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H11F3NO6P
#4: 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
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.4 % / Description: plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50 mM Bicine-NaOH, pH 7.8; 10% PEG 8,000; 2 mM spermine
PH range: 7.6 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 24, 2013
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→20.95 Å / Num. all: 72402 / Num. obs: 72402 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.9
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.15data extraction
REFMAC5.8.0073refinement
MOLREP11.0.02phasing
SCALA3.3.21data scaling
iMOSFLM7.1.1data reduction
CrystalCleardata collection
d*TREKdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4KKX

4kkx


Resolution: 1.75→20.95 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1792 / WRfactor Rwork: 0.148 / FOM work R set: 0.8467 / SU B: 4.753 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1005 / SU Rfree: 0.0972 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1885 3601 5 %RANDOM
Rwork0.1584 68775 --
obs0.1603 72402 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.87 Å2 / Biso mean: 26.729 Å2 / Biso min: 10.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0 Å20.04 Å2
2--0.1 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 1.75→20.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4905 0 90 617 5612
Biso mean--32.42 35.23 -
Num. residues----648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195274
X-RAY DIFFRACTIONr_bond_other_d0.0010.025021
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.9857150
X-RAY DIFFRACTIONr_angle_other_deg0.872311572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7645681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51624.167228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69615872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6971534
X-RAY DIFFRACTIONr_chiral_restr0.1050.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216090
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021189
X-RAY DIFFRACTIONr_mcbond_it1.4841.7342679
X-RAY DIFFRACTIONr_mcbond_other1.4731.7312678
X-RAY DIFFRACTIONr_mcangle_it2.2842.5853375
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 240 -
Rwork0.317 5055 -
all-5295 -
obs--99.89 %
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
11.3996-0.85640.26931.2827-0.60870.79860.2373-0.3020.158-0.237-0.158-0.096-0.12540.2327-0.07930.1552-0.05430.07580.2344-0.05440.0409A052.306141.354111.4993
20.84160.29310.2140.14420.1271.19-0.005-0.13070.10030.0195-0.03250.0292-0.1507-0.0940.03760.04820.00490.01620.0843-0.03960.0881A136.463847.851413.7519
31.22450.5743-0.15030.85850.08080.32460.1145-0.01230.0887-0.0045-0.0770.0417-0.0720.0011-0.03760.029-0.0070.02660.09440.01480.071A238.565342.49174.5339
40.80960.21850.00910.4052-0.24250.54090.0453-0.0611-0.0972-0.0398-0.0323-0.0559-0.03870.0318-0.0130.0265-0.01280.00470.13010.00860.0526A341.534328.26959.9308
50.5109-0.9721-0.11885.98072.05660.84420.0691-0.1303-0.04660.34590.1438-0.41470.19250.012-0.21290.0642-0.0399-0.06310.18440.01320.0665A452.057328.689221.6269
66.0927-4.02152.48196.0327-0.13651.6885-0.22390.03050.26570.03170.0591-0.0798-0.17920.07390.16480.1223-0.0959-0.04530.12030.01070.033A549.965854.248219.7889
70.30280.1168-0.25730.4346-0.19860.57910.0086-0.0095-0.0772-0.0422-0.0334-0.02390.06290.23150.02480.01850.0298-0.01790.18210.0070.0476B627.821316.852120.0124
80.3737-0.0093-0.09020.0099-0.04480.2551-0.042-0.05470.0132-0.00180.0053-0.00980.0269-0.02960.03680.016-0.0017-0.01830.13580.00720.0462B73.229514.787727.6266
90.89680.0327-0.76690.4649-0.12250.69190.1519-0.01940.13520.0179-0.00990.0374-0.12420.0474-0.1420.0328-0.00930.00770.1562-0.0020.0603B817.694531.142530.8945
100.31350.0288-0.09150.0231-0.06090.19250.00520.0210.02670.0011-0.0026-0.0120.0063-0.0175-0.00260.0154-0.0054-0.00810.12810.00180.0506B95.207722.910313.338
110.15540.1954-0.11870.47220.23220.81180.07430.03040.0170.05950.0483-0.034-0.1014-0.1156-0.12260.03790.00980.01710.1570.0190.0309B10-6.934928.319617.8261
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 29
2X-RAY DIFFRACTION2A30 - 77
3X-RAY DIFFRACTION3A78 - 110
4X-RAY DIFFRACTION4A111 - 178
5X-RAY DIFFRACTION5A194 - 216
6X-RAY DIFFRACTION6A248 - 268
7X-RAY DIFFRACTION7B2 - 37
8X-RAY DIFFRACTION8B38 - 100
9X-RAY DIFFRACTION9B101 - 196
10X-RAY DIFFRACTION10B197 - 364
11X-RAY DIFFRACTION11B365 - 395

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