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- PDB-6vfd: Tryptophan synthase mutant Q114A in complex with cesium ion at th... -

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Basic information

Entry
Database: PDB / ID: 6vfd
TitleTryptophan synthase mutant Q114A in complex with cesium ion at the metal coordination site and 2-aminophenol quinonoid at the enzyme beta site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / protein complex
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. / 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
Chem-1D0 / : / SERINE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain / 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. / Fan, L. / Dunn, M.F. / Mueller, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)2R01GM097569-06A1 United States
CitationJournal: To be Published
Title: Tryptophan synthase mutant Q114A in complex with cesium ion at the metal coordination site and 2-aminophenol quinonoid at the enzyme beta site.
Authors: Hilario, E. / Fan, L. / Dunn, M.F. / Mueller, L.J.
History
DepositionJan 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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)74,19238
Polymers71,5612
Non-polymers2,63136
Water12,611700
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)148,38376
Polymers143,1214
Non-polymers5,26272
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area17480 Å2
ΔGint-387 kcal/mol
Surface area44280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.079, 59.340, 67.440
Angle α, β, γ (deg.)90.000, 94.850, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-416-

CS

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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 / Details (production host): mutant beta-Q114A / Production host: Escherichia coli (E. coli) / Strain (production host): CB149
References: UniProt: A0A0D6FWC1, UniProt: P00929*PLUS, tryptophan synthase
#2: Protein Tryptophan synthase beta chain / Tryptophan synthase beta chain (EC) / Tryptophan synthase subunit beta


Mass: 42861.828 Da / Num. of mol.: 1 / Mutation: Q114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: trpB, AAP89_02045, ABO94_19170, AF480_03975, AF488_06015, AF489_02660, AIC76_02215, AU613_22485, AXR84_21850, AXU58_18720, C2253_17845, CD48_01255, CE87_00490, CET98_00490, CQG18_02715, CVR97_ ...Gene: trpB, AAP89_02045, ABO94_19170, AF480_03975, AF488_06015, AF489_02660, AIC76_02215, AU613_22485, AXR84_21850, AXU58_18720, C2253_17845, CD48_01255, CE87_00490, CET98_00490, CQG18_02715, CVR97_02985, D4369_03495, D4380_02480, D4401_03780, D4E62_00155, D6360_05135, D7F20_01770, D7H43_22440, DD95_04150, DJ388_09100, DKJ11_03255, DKU57_01740, DLM31_00170, DNV30_02640, DO698_02865, DOJ90_01720, DOQ88_05395, DQ848_22185, DRM14_00170, DSF69_00170, DSR36_00155, DUW48_00170, E2F01_02625, EBO41_01950, EBP31_03920, EGU67_04975, EHB24_02705, EHC98_05585, EIW53_01745, F0A00_14785, F0A01_15745, F0A02_08960, F0A03_20195, F0A04_22070, F0A05_01740, F0A06_01905, F0A07_12870, F0A08_01425, F0U66_12100, FKA80_16460, FKA81_16995, FKA82_17080, FKA83_17705, FKA84_18900, FKA85_16755, FKA86_15095, FKA87_20420, FKA88_00465, FKA89_17495, FKA90_04050, FKA91_03380, FKA92_00475, FKA93_04425, FKA94_02440, FKA95_00475, FKA96_03185, FKA97_05420, FKA98_04655, FKA99_00465, FKB00_08210, FKB01_00475, FKB02_00470, FKB03_06095, FKB12_08200, FKB15_09545, FKB19_17260, FYL57_17810, FYL66_01025, FYL68_08225, FYL69_04355, FYL71_20365, FYL73_06975, FYL74_10415, FYL75_12085, FYL77_17200, FYL81_18315, FYL84_11395, FYL90_05690, FYL92_04810, FYL93_03130, FYL94_11585, FYL96_18520, FYM06_17485, FYM08_08630, FYM09_19335, FYM12_03600, FYM54_08665, FZ992_19115, FZ993_02220, FZ994_08290, FZ995_12310, FZ996_09230, FZ997_15170, FZ998_14625, FZ999_17455, GW08_03175, JO10_00490, LZ63_02660, NG18_14010, NU83_02660, QA89_14465, QB40_00170, QD15_05225, RJ78_16500, SAMEA4398682_02247, UPM260_1493, Y934_00965, YG50_13195, YI33_00155, YR17_00170, YT65_03520, ZA53_18735, ZB89_05455, ZC54_00170
Plasmid: PEBA-10 / Details (production host): mutant beta-Q114A / Production host: Escherichia coli (E. coli) / Strain (production host): CB149
References: UniProt: A0A5K1VAP1, UniProt: P0A2K1*PLUS, tryptophan synthase

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Non-polymers , 7 types, 736 molecules

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


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


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-1D0 / (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid


Mass: 425.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N3O8P / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cs
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / 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: 51.77 % / Description: large plate-like crystal (200 x 100 x 100)
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 50 mM Bicine-CsOH, 10% PEG 8,000, 4 mM spermine / 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: Sep 28, 2018 / Details: Varimax Confocal Max-Flux
RadiationMonochromator: Osmic Varimax HF ArcSec / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→91.212 Å / Num. all: 93786 / Num. obs: 93786 / % possible obs: 98.5 % / Redundancy: 3.4 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.077 / Rsym value: 0.065 / Net I/av σ(I): 6.5 / Net I/σ(I): 8.7 / Num. measured all: 316674
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
1.6-1.693.20.36239804126180.2420.4360.36291
1.69-1.793.30.2592.843066129610.1680.310.2592.999.1
1.79-1.913.30.193.740547122720.1220.2270.194.199.5
1.91-2.073.30.1325.238003114530.0840.1570.1326.499.9
2.07-2.263.40.0996.835468105450.0630.1180.0999100
2.26-2.533.40.0778.53269695800.0480.0910.07710.9100
2.53-2.923.50.0659.82984584510.040.0770.06513.8100
2.92-3.583.60.05710.72593771950.0340.0660.05718.3100
3.58-5.063.60.04613.22025755810.0280.0540.04621.8100
5.06-36.8983.50.04911.31105131300.030.0570.04920.399.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.495
Highest resolutionLowest resolution
Rotation36.9 Å1.87 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 93268
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.67-10035.80.911634
6.13-8.67410.8941138
5.01-6.1339.20.8781456
4.34-5.0130.10.9131705
3.88-4.3427.80.9121922
3.54-3.8826.40.9212117
3.28-3.5426.20.9052307
3.07-3.2826.90.8912440
2.89-3.0727.50.8852623
2.74-2.8926.60.8792752
2.61-2.7425.60.8882888
2.5-2.6126.50.8862977
2.41-2.525.10.883151
2.32-2.4125.30.8783272
2.24-2.3223.30.8953335
2.17-2.2423.20.8933483
2.1-2.1724.20.8883605
2.04-2.123.70.8783691
1.99-2.0426.40.8713862
1.94-1.9925.90.8563940
1.89-1.9426.60.8524008
1.85-1.8927.20.8364086
1.81-1.8527.70.8314260
1.77-1.8129.10.8424242
1.73-1.7728.20.8324363
1.7-1.7329.80.8294454
1.67-1.731.60.8044542
1.64-1.6733.40.7844613
1.6-1.6442.40.7165402

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Processing

Software
NameVersionClassification
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
MOLREP7.0.078phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HPJ

4hpj


Resolution: 1.7→29.69 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.475 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.109 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 3952 5 %RANDOM
Rwork0.1945 ---
obs0.1959 75065 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.1 Å2 / Biso mean: 30.43 Å2 / Biso min: 12.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å2-0 Å2-0.05 Å2
2---0.31 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 1.7→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4903 0 119 733 5755
Biso mean--43.16 39.01 -
Num. residues----648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125254
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.6327116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3135682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54122.031261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44115873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0521533
X-RAY DIFFRACTIONr_chiral_restr0.0870.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024059
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 350 -
Rwork0.281 5423 -
all-5773 -
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)
15.4314-1.0227-0.31872.1670.02182.03590.1115-0.26650.16520.2553-0.0723-0.31530.11990.4026-0.03930.2245-0.0877-0.01990.17340.03380.289951.87512.076711.9259
22.20631.1621-0.52963.2863-0.12410.87150.2411-0.14940.27720.23-0.17640.0913-0.210.0464-0.06470.0965-0.0340.03840.09090.00410.156437.78369.98188.6885
31.599-0.1399-1.59266.4578-1.18075.7879-0.0079-0.2686-0.2080.1497-0.2819-0.12760.25920.17150.28980.1105-0.0423-0.08570.21690.04860.23946.4692-4.829116.006
41.42210.0410.69214.67850.79421.6616-0.0882-0.3707-0.2050.90640.01960.13990.17060.26540.06860.3343-0.0166-0.08030.39760.02860.342652.24783.03923.4314
54.2399-3.25350.19547.25471.31390.4706-0.0367-0.1797-0.08750.3690.03980.10730.0445-0.0503-0.00310.35660.00070.01210.224-0.02830.305337.407624.114422.7378
66.4247-6.04923.60255.9447-3.36922.59940.0282-0.03540.48010.1134-0.0291-0.3784-0.180.15880.00090.3376-0.0662-0.02210.2549-0.0430.392249.320924.366720.9129
72.14920.8303-0.87960.9899-0.87782.61330.0135-0.1189-0.25150.0864-0.0896-0.2462-0.02070.39990.07610.0530.0203-0.02760.10130.01010.08127.6658-12.87519.6785
80.7812-0.0435-0.1480.9065-0.33162.30310.0442-0.2596-0.1308-0.0033-0.0396-0.02750.2207-0.1807-0.00460.0389-0.0415-0.00770.11840.05040.02551.2029-17.46127.9035
91.03270.34460.3640.61480.48592.57160.0482-0.2250.0317-0.00110.0008-0.0712-0.25020.2342-0.0490.0596-0.02970.00890.1013-0.01160.023710.2106-8.528230.3866
101.3470.5988-0.75430.9288-0.51062.8020.15660.09960.2939-0.0093-0.02850.1496-0.64030.0259-0.12810.363-0.05440.01870.1316-0.01090.192313.6497.161932.1052
112.89240.454-0.27960.7005-0.07861.65630.0832-0.17170.06940.0334-0.0803-0.0439-0.06580.207-0.00290.04630.0069-0.00380.046-0.00130.006812.5555-11.310221.2453
121.21990.153-0.02473.5356-0.70041.3619-0.03170.09740.022-0.3139-0.0026-0.09980.00420.03940.03430.03740.00660.00090.0340.00370.02315.9471-4.20187.4932
133.97630.34120.37694.4893-0.9040.23550.06090.09590.72090.0784-0.07020.2957-0.0220.03760.00940.0879-0.00830.04570.12530.01010.153420.80482.89438.4295
142.4539-1.1664-0.21430.84170.27741.21820.0516-0.02290.2686-0.00590.046-0.1993-0.0860.1099-0.09770.01870.0040.00890.03480.00160.058111.1475-3.988111.3209
151.30060.5627-0.46750.8105-0.07942.20050.01110.05750.12320.01310.00280.0784-0.1151-0.2201-0.01390.02520.014-0.01010.02350.0020.0215-6.3773-2.885413.8764
162.1510.22950.89021.59240.64753.7091-0.0441-0.11590.410.12670.03850.1757-0.4533-0.18070.00560.09190.00860.03060.08490.00630.1061-6.9124-0.342618.6466
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 29
2X-RAY DIFFRACTION2A30 - 159
3X-RAY DIFFRACTION3A160 - 177
4X-RAY DIFFRACTION4A193 - 234
5X-RAY DIFFRACTION5A235 - 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 - 273
13X-RAY DIFFRACTION13B274 - 295
14X-RAY DIFFRACTION14B296 - 322
15X-RAY DIFFRACTION15B323 - 365
16X-RAY DIFFRACTION16B366 - 396

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