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- PDB-4hn4: Tryptophan synthase in complex with alpha aminoacrylate E(A-A) fo... -

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Basic information

Entry
Database: PDB / ID: 4hn4
TitleTryptophan synthase in complex with alpha aminoacrylate E(A-A) form and the F9 inhibitor in the alpha site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE INHIBITOR / Lyase / carbon-oxygen lyase / tryptophan biosynthesis / Salmonella / F9F / Allosteric enzyme / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / Pyridoxal phosphate / alpha amino acrylate / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / 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 / 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-0JO / : / Chem-F9F / DI(HYDROXYETHYL)ETHER / 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: 1.64 Å
AuthorsHilario, E. / Niks, D. / Dunn, M.F. / Mueller, L.J. / Fan, L.
CitationJournal: Biochemistry / Year: 2013
Title: Allostery and substrate channeling in the tryptophan synthase bienzyme complex: evidence for two subunit conformations and four quaternary states.
Authors: Niks, D. / Hilario, E. / Dierkers, A. / Ngo, H. / Borchardt, D. / Neubauer, T.J. / Fan, L. / Mueller, L.J. / Dunn, M.F.
History
DepositionOct 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Sep 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_special_symmetry / struct_conn / struct_site
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 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)73,37312
Polymers71,6182
Non-polymers1,75510
Water12,178676
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)146,74624
Polymers143,2354
Non-polymers3,51020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8700 Å2
ΔGint-35 kcal/mol
Surface area42720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.970, 59.720, 67.400
Angle α, β, γ (deg.)90.000, 94.690, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-919-

HOH

21B-922-

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
Details: Yang et al (1996) Protein Expression and Purification, 8:126-136.
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: STM1727, trpA, trpA and trpB / 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: 42918.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 6 types, 686 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-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N2O7P
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#7: Chemical ChemComp-CS / CESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 676 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 50 mM Bicine-CsOH, 10% PEG 8000, 2 mM Spermine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Jan 1, 2012 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 3.3 % / Av σ(I) over netI: 9.6 / Number: 283827 / Rsym value: 0.049 / D res high: 1.635 Å / D res low: 91.677 Å / Num. obs: 86376 / % possible obs: 95.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.1730.7499.610.0380.0383.6
3.665.1710010.0340.0343.6
2.993.6610010.0430.0433.6
2.592.9910010.0490.0493.5
2.312.5910010.0560.0563.4
2.112.3199.910.0670.0673.2
1.952.119810.0850.0853
1.831.9593.810.1170.1173.1
1.721.8389.810.1560.1563.2
1.631.7287.310.220.223.3
ReflectionResolution: 1.63→30.74 Å / Num. all: 90177 / Num. obs: 86376 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 12.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.74 Å
Translation2.5 Å30.74 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TJP

1tjp


Resolution: 1.64→28.59 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.2035 / WRfactor Rwork: 0.154 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.856 / SU B: 3.755 / SU ML: 0.058 / SU R Cruickshank DPI: 0.1146 / SU Rfree: 0.0914 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2004 4281 5 %RANDOM
Rwork0.1478 ---
all0.1478 89395 --
obs0.1504 85601 95.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.29 Å2 / Biso mean: 21.4911 Å2 / Biso min: 9.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20.06 Å2
2--0.45 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.64→28.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5009 0 99 676 5784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195343
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9897249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6415705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73223.939231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67315895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6711538
X-RAY DIFFRACTIONr_chiral_restr0.0980.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214071
X-RAY DIFFRACTIONr_rigid_bond_restr3.1235343
X-RAY DIFFRACTIONr_sphericity_free29.3635179
X-RAY DIFFRACTIONr_sphericity_bonded15.20955729
LS refinement shellResolution: 1.64→1.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 277 -
Rwork0.281 5247 -
all-5524 -
obs--87.07 %
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)
11.4270.5498-0.541.17160.05470.4282-0.02380.1216-0.067-0.0341-0.01350.09060.0016-0.06820.03730.04380.006-0.0090.0164-0.00730.0552-53.8426-0.188621.3054
20.01220.01020.00370.0258-0.00140.00260.0024-0.00110.00240.0009-0.0025-0.00060.0007-0.00170.00010.0490.0003-0.00420.01450.00010.0596-40.1996-2.98925.3038
30.17370.022-0.04070.1609-0.05440.09520.00190.0096-0.007-0.0069-0.00870.0082-0.0067-0.00180.00680.04810.0001-0.0070.0109-0.00140.0616-48.6364-13.176511.2059
40.16960.11830.0020.259-0.03050.00640.00830.00390.00910.0166-0.0060.0143-0.0057-0.0006-0.00230.04940.0026-0.00380.0151-0.00050.0595-48.83114.534511.5616
50.0897-0.0439-0.05250.0220.02660.03320.00310.0055-0.00540.0014-0.00450.0050.0038-0.00840.00140.0501-0.0012-0.0060.013800.0596-30.3849-25.979113.9233
60.02620.05040.06940.09890.1340.18440.00430.0056-0.00660.00570.0077-0.00480.01010.016-0.0120.04830.0011-0.00530.0130.00050.0617-4.0741-30.79045.5349
70.01530.00180.0010.00080.00310.0196-0.00020.00040.001-0.0008-0.0005-0.0001-0.0016-0.00080.00070.04950.0001-0.00470.01280.00020.0593-11.7757-17.917113.6137
80.0491-0.07450.13180.1729-0.21110.3576-0.010.01030.0050.016-0.0117-0.0137-0.03430.02560.02160.0504-0.002-0.00340.01530.00150.05814.1706-14.282415.4848
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 29
2X-RAY DIFFRACTION2A30 - 159
3X-RAY DIFFRACTION3A160 - 202
4X-RAY DIFFRACTION4A203 - 268
5X-RAY DIFFRACTION5B2 - 37
6X-RAY DIFFRACTION6B38 - 70
7X-RAY DIFFRACTION7B71 - 364
8X-RAY DIFFRACTION8B365 - 396

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