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- PDB-6c73: Tryptophan synthase Q114A mutant (internal aldimine state) in com... -

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Basic information

Entry
Database: PDB / ID: 6c73
TitleTryptophan synthase Q114A mutant (internal aldimine state) in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) with cesium ion bound in the metal coordination site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / F9F ligand / cesium ion / mutant beta-Q114A
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 / 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-F9F / 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: 1.65 Å
AuthorsHilario, E. / Dunn, M.F. / Mueller, L.J. / Fan, L.
CitationJournal: To be Published
Title: Tryptophan synthase Q114A mutant (internal aldimine state) in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) with cesium ion bound in the metal coordination site.
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J. / Fan, L.
History
DepositionJan 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Sep 29, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_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_asym_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_type.id
Revision 1.4Oct 4, 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)74,47535
Polymers71,3162
Non-polymers3,15933
Water15,547863
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)148,95070
Polymers142,6334
Non-polymers6,31766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8570 Å2
ΔGint-32 kcal/mol
Surface area44630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.609, 58.980, 67.150
Angle α, β, γ (deg.)90.000, 94.400, 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)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpA, STM1727 / Plasmid: PEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase
#2: Protein Tryptophan synthase beta chain


Mass: 42617.480 Da / Num. of mol.: 1 / Mutation: Q114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: trpB, STM1726 / Plasmid: PEBA-10 / Details (production host): mutant Q114A / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 8 types, 896 molecules

#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: 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
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cs
#8: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 863 / 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: 2.51 Å3/Da / Density % sol: 51.07 % / Description: large plate-like crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 100 mM Bicine-CsOH, pH 7.8, 5-10% PEG8000, 1 mM DTT, 1 mM EDTA, 2 mM F9F
PH range: 7.6-8.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen flow
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 7, 2017 / Details: VariMax
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 85206 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 11.917 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.032 / Rrim(I) all: 0.062 / Rsym value: 0.041 / Net I/av σ(I): 12.9 / Net I/σ(I): 15.1
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
1.65-1.743.40.183.9123230.9610.1350.2530.1899.6
1.74-1.843.40.1265.6117360.0940.1770.12699.9
1.84-1.973.40.097.7110270.0670.1260.09100
1.97-2.133.50.06510.7102850.0490.0930.065100
2.13-2.333.60.04913.894770.0380.0720.049100
2.33-2.613.60.04116.285640.0320.0620.041100
2.61-3.013.70.03916.475800.030.0580.039100
3.01-3.693.70.03617.564610.0260.0510.036100
3.69-5.223.70.02449970.020.0380.024100
5.22-19.813.60.02227560.0230.0440.02298.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.382
Highest resolutionLowest resolution
Rotation19.82 Å1.8 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
MOLREP11.6.02phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
iMOSFLM7.2.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HT3

4ht3


Resolution: 1.65→19.82 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.314 / SU ML: 0.051 / SU R Cruickshank DPI: 0.1211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.086 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1829 4306 5.1 %RANDOM
Rwork0.1383 ---
obs0.1406 80889 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 89.32 Å2 / Biso mean: 18.708 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.02 Å2
2--0.02 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.65→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5005 0 150 917 6072
Biso mean--27.89 32.15 -
Num. residues----663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195567
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9897552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5824.163233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47515921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4091536
X-RAY DIFFRACTIONr_chiral_restr0.1020.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214257
X-RAY DIFFRACTIONr_rigid_bond_restr2.37335567
X-RAY DIFFRACTIONr_sphericity_free27.9375227
X-RAY DIFFRACTIONr_sphericity_bonded9.06456153
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 320 -
Rwork0.225 5862 -
all-6182 -
obs--99.53 %
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)
10.12910.04270.0770.33870.03490.17360.01870.01170.0091-0.008-0.01490.0156-0.00510.0018-0.00370.0408-0.00520.0160.02410.0070.044337.860410.02268.8869
20.5457-0.19960.0380.60010.35070.30090.0228-0.1119-0.08290.03640.04640.01660.07670.001-0.06910.0595-0.0025-0.04930.02330.01310.070547.1109-1.597921.7771
30.1731-0.01840.24260.71170.43750.66150.0436-0.02560.01750.0404-0.003-0.08470.0757-0.025-0.04060.04-0.0144-0.01140.04-0.00770.04351.3526.699322.9123
41.892-1.41170.26296.9934-0.69150.07830.0633-0.12810.04960.1986-0.0814-0.1069-0.0139-0.00490.01810.06610.00490.0030.0236-0.01250.037437.417924.479523.1137
53.0183-2.49770.70372.9359-0.13560.4022-0.0906-0.04450.20330.06530.0601-0.1786-0.04650.01050.03050.069-0.02490.00040.0115-0.00650.05749.284624.400321.1961
60.3923-0.0194-0.42770.00150.02020.5001-0.0239-0.0409-0.0397-0.00330.00110.00290.03780.08240.02280.03860.0046-0.01550.06190.00120.040827.836-13.150619.3565
70.0309-0.0416-0.01410.2036-0.13590.1847-0.0241-0.0069-0.00190.00470.0222-0.00930.042-0.04160.00190.0388-0.0055-0.00420.06270.00980.02481.354-17.638127.8067
80.01260.04310.01650.16550.06540.02720.01160.0051-0.00070.0251-0.0069-0.01160.0119-0.0112-0.00460.04540.0055-0.00860.06120.01190.022610.558-8.700630.2135
90.12090.22330.20260.46220.21190.87720.01650.02250.00190.06690.05680.0276-0.13510.0139-0.07320.05640.00870.03820.02790.02050.045914.30877.163232.2552
100.07280.0431-0.02520.11540.1130.196-0.0098-0.0128-0.0177-0.0068-0.0006-0.00770.01430.02040.01040.0429-0.0009-0.00890.04930.00740.032712.8717-11.430421.1607
110.05070.02550.07850.6693-0.19260.2194-0.01130.03250.0128-0.0232-0.01290.01170.00070.04550.02420.04570.00120.00150.04620.00490.03455.9126-4.21097.5083
120.75420.0603-0.17930.8729-0.52790.35250.0523-0.01060.1418-0.0287-0.02260.030.01840.0231-0.02980.0382-0.00450.01010.03270.01820.073820.82483.04098.9535
130.5483-0.3421-0.15360.26250.2020.27850.015-0.01910.0504-0.00650.0283-0.04630.00890.024-0.04330.036-0.00860.00210.05690.00340.027611.2068-4.276711.6063
140.27260.0571-0.00390.0426-0.08650.2465-0.0080.0080.0140.00490.01430.003-0.0329-0.0309-0.00630.04720.002-0.00080.04880.00440.0279-6.387-2.977613.8906
150.13420.19280.13660.29490.18620.53640.014-0.00920.02550.02970.01140.0501-0.0533-0.0567-0.02550.04730.01480.01390.06160.00770.0269-6.9634-0.38418.472
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 159
2X-RAY DIFFRACTION2A160 - 202
3X-RAY DIFFRACTION3A203 - 234
4X-RAY DIFFRACTION4A235 - 247
5X-RAY DIFFRACTION5A248 - 268
6X-RAY DIFFRACTION6B2 - 37
7X-RAY DIFFRACTION7B38 - 70
8X-RAY DIFFRACTION8B71 - 126
9X-RAY DIFFRACTION9B127 - 165
10X-RAY DIFFRACTION10B166 - 244
11X-RAY DIFFRACTION11B245 - 273
12X-RAY DIFFRACTION12B274 - 295
13X-RAY DIFFRACTION13B296 - 322
14X-RAY DIFFRACTION14B323 - 365
15X-RAY DIFFRACTION15B366 - 396

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