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- PDB-6duc: Crystal structure of mutant beta-K167T tryptophan synthase in com... -

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Basic information

Entry
Database: PDB / ID: 6duc
TitleCrystal structure of mutant beta-K167T tryptophan synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, cesium ion at the metal coordination site, and 2-aminophenol quinonoid (1D0) at the beta-site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / F9F / 1D0 / Cesium ion / mutant beta-K167T / lyase / lyase inhibitor / 2-aminophenol quinonoid / Salmonella typhimurium / 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. / 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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-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-1D0 / 2-AMINOPYRIDINE / : / Chem-F9F / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.791 Å
AuthorsHilario, E. / Dunn, M.F. / Mueller, L.J. / Fan, L.
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 Q114A mutant in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate (P1T) at the beta site, and ...Title: Tryptophan synthase Q114A mutant in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate (P1T) at the beta site, and cesium ion at the metal coordination site.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J. / Fan, L.
History
DepositionJun 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)73,91928
Polymers71,5902
Non-polymers2,32926
Water9,350519
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)147,83856
Polymers143,1794
Non-polymers4,65952
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area17160 Å2
ΔGint-348 kcal/mol
Surface area42600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.261, 60.044, 67.298
Angle α, β, γ (deg.)90.000, 94.650, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-412-

CS

21B-678-

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 (bacteria) / Gene: trpA, DD95_04145 / Plasmid: PEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149
References: UniProt: A0A0D6FWC1, UniProt: P00929*PLUS, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42890.805 Da / Num. of mol.: 1 / Mutation: K167T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: trpB, DD95_04150 / Plasmid: PEBA-10 / Details (production host): mutant beta-K167T / Production host: Escherichia coli (E. coli) / Strain (production host): CB149
References: UniProt: A0A0J0ZFZ1, UniProt: P0A2K1*PLUS, tryptophan synthase

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Non-polymers , 8 types, 545 molecules

#3: Chemical ChemComp-F9F / 2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE / N-(4'-TRIFLUOROMETHOXYBENZENESULFONYL)-2-AMINO-1-ETHYLPHOSPHATE, F9


Mass: 365.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11F3NO7PS
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / 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
#8: Chemical ChemComp-2AP / 2-AMINOPYRIDINE


Mass: 95.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7N2
#9: Chemical ChemComp-CS / CESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.6 Å3/Da / Density % sol: 52.7 % / Description: Large plate-like crystal
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 50 mM Bicine-Cs, 10-12% PEG3350, 50 mM cesium chloride, 4-8 mM spermine
PH range: 7.8-8.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryo-Jet crystal cryocoolers
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 27, 2018 / Details: Bent cylinders, stripes of Pt, Rh, and clear
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.791→91.827 Å / Num. obs: 67697 / % possible obs: 98.9 % / Redundancy: 8 % / Biso Wilson estimate: 16.76 Å2 / CC1/2: 0.945 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.084 / Rrim(I) all: 0.24 / Rsym value: 0.215 / Net I/av σ(I): 1.7 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.8-1.94.40.5221.193570.7970.2990.6590.52294.3
1.9-2.018.20.6790.593840.2810.770.67999.7
2.01-2.158.90.4820.888710.1850.5310.482100
2.15-2.328.30.36182010.1440.4020.3699.7
2.32-2.558.20.2791.575630.1130.3140.27999.9
2.55-2.859.30.2411.469110.0930.2670.241100
2.85-3.298.70.1862.660590.0710.2050.18699.8
3.29-4.028.20.1732.351620.0690.1940.17399.7
4.02-5.699.10.1433.540100.0510.1560.14399.9
5.69-19.7038.30.1094.121790.0390.120.10996.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.46 Å19.7 Å
Translation6.46 Å19.7 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 67337
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.11-10041.30.909515
6.66-9.1145.10.875842
5.5-6.6643.70.8771047
4.79-5.538.50.9031255
4.3-4.7929.60.9131391
3.93-4.3280.9041544
3.65-3.93270.9031676
3.42-3.6525.20.8981778
3.23-3.4226.40.8941867
3.06-3.2326.50.91994
2.92-3.0627.40.8882099
2.8-2.9225.90.8792206
2.69-2.826.80.8782273
2.59-2.6925.50.8872363
2.51-2.59250.9052442
2.43-2.5125.60.8892546
2.36-2.4324.50.8932638
2.29-2.3623.60.8922668
2.23-2.2922.50.8962734
2.17-2.2322.30.8972837
2.12-2.1723.10.8862911
2.07-2.1222.50.8822960
2.03-2.0723.30.8623045
1.99-2.0325.10.8423092
1.95-1.9926.40.7943181
1.91-1.9529.80.7063217
1.87-1.91320.6343102
1.84-1.8734.60.6113145
1.8-1.8443.20.5683969

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Processing

Software
NameVersionClassification
MOSFLM7.2.1data reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
DM7.0.058phasing
PHENIX1.13-2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HPJ

4hpj


Resolution: 1.791→19.703 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.92
RfactorNum. reflection% reflection
Rfree0.2315 3515 5.2 %
Rwork0.1853 --
obs0.1877 67592 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.64 Å2 / Biso mean: 30.5544 Å2 / Biso min: 7.02 Å2
Refinement stepCycle: final / Resolution: 1.791→19.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4926 0 109 553 5588
Biso mean--35.96 37.08 -
Num. residues----660
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7909-1.81550.34811010.32281872197371
1.8155-1.84140.31951200.27512462258294
1.8414-1.86880.29431150.27292442255793
1.8688-1.8980.30761560.27422366252293
1.898-1.92910.32511190.2522637275699
1.9291-1.96230.28451360.229425932729100
1.9623-1.9980.27461300.208126292759100
1.998-2.03640.25011530.202425712724100
2.0364-2.07790.24811510.19626012752100
2.0779-2.1230.24791430.188225712714100
2.123-2.17240.22191510.1826272778100
2.1724-2.22660.22941570.176426042761100
2.2266-2.28670.21871450.17452571271699
2.2867-2.35390.20351530.170425852738100
2.3539-2.42980.23551390.174826282767100
2.4298-2.51640.25711320.185226162748100
2.5164-2.6170.21941570.180126212778100
2.617-2.73580.24691350.183426102745100
2.7358-2.87960.24321650.179525752740100
2.8796-3.05940.22721490.174926512800100
3.0594-3.29460.2221470.171926022749100
3.2946-3.62430.22811470.17352613276099
3.6243-4.14450.20061480.159726332781100
4.1445-5.20570.1921410.15426732814100
5.2057-19.70460.20741250.19052724284999
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)
10.00440.01090.00160.011-0.00480.00070.10290.0330.01490.0483-0.04370.01860.02220.03450-0.1118-0.1140.08770.11110.08190.132740.147510.31848.8371
20.001600.00060.001-0.0010.00040.012-0.0039-0.01390.0157-0.0033-0.0008-0.01010.006700.1726-0.021-0.07780.22810.0460.255946.3313-1.374121.1162
30.00510.00510.00060.00220.000300.0153-0.0138-0.00890.0107-0.0002-0.0003-0.01750.000200.2587-0.1059-0.03650.27420.05760.288846.702817.480621.5062
40.0016-0.0019-0.0014-0.0012-0.00120.00060.0277-0.0023-0.02380.00590.0042-0.0128-0.00330.012600.04990.0388-0.01840.11810.02830.055727.78-12.942319.7619
50.00320.0004-0.00690.0018-0.00370.0031-0.02340.0062-0.01020.0352-0.0289-0.00380.0312-0.017700.0390.0106-0.02960.06550.02770.00151.664-17.618928.2837
6-0.00530.00340.0013-0.0029-0.00630.00810.1513-0.0050.0058-0.05690.08160.0176-0.03630.0154-0-0.0338-0.01370.15940.052-0.0332-0.290514.0387-1.701929.346
70.00050.00450.00880.00740.00080.01840.03430.01180.15620.0262-0.03040.00040.0771-0.015600.03430.0224-0.0096-0.00160.0355-0.00395.2557-6.936812.9337
8-0.00030.0023-0.0014-0.0002-0.00140.00310.0233-0.0016-0.00640.00120.01480.0005-0.0006-0.008600.06440.00740.00940.03740.01370.0207-6.4509-1.973518.4669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 159 )A1 - 159
2X-RAY DIFFRACTION2chain 'A' and (resid 160 through 202 )A160 - 202
3X-RAY DIFFRACTION3chain 'A' and (resid 203 through 268 )A203 - 268
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 37 )B2 - 37
5X-RAY DIFFRACTION5chain 'B' and (resid 38 through 70 )B38 - 70
6X-RAY DIFFRACTION6chain 'B' and (resid 71 through 196 )B71 - 196
7X-RAY DIFFRACTION7chain 'B' and (resid 197 through 365 )B197 - 365
8X-RAY DIFFRACTION8chain 'B' and (resid 366 through 395 )B366 - 395

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