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- PDB-6dz4: Crystal structure of Salmonella typhimurium Tryptophan Synthase w... -

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Database: PDB / ID: 6dz4
TitleCrystal structure of Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site and (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine at the beta-site
Components(Tryptophan synthase ...) x 2
KeywordsLYASE/LYASE Inhibitor / F9F / LYASE-LYASE Inhibitor 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. / 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-KOU / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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: Crystal structure of Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site and (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)- ...Title: Crystal structure of Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site and (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine at the beta site
Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J. / Fan, L.
History
DepositionJul 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0May 6, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct / struct_keywords / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.title / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct.title / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 3.0Jun 10, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / computing / diffrn / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_validate_close_contact / refine / refine_hist / reflns / reflns_shell / struct_asym / struct_conn / struct_keywords / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _diffrn.ambient_temp_details / _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_close_contact.auth_seq_id_1 / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_FOM_work_R_set / _refine.overall_SU_R_free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.pdbx_B_iso_mean_ligand / _reflns.number_all / _reflns_shell.number_measured_all / _reflns_shell.pdbx_netI_over_sigmaI_obs / _struct_asym.entity_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_keywords.text / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id / _struct_site_gen.symmetry
Description: Model orientation/position
Details: We have flipped the side chain of residue Q114 from chain B and the current orientation makes more sense regarding local hydrogen bonding.
Provider: author / Type: Coordinate replacement
Revision 3.1Oct 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_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)73,21925
Polymers71,6182
Non-polymers1,60123
Water13,295738
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)146,43850
Polymers143,2354
Non-polymers3,20346
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14350 Å2
ΔGint-158 kcal/mol
Surface area44610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.509, 59.300, 67.325
Angle α, β, γ (deg.)90.000, 94.690, 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 typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (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: 42918.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpB, STM1726 / Plasmid: PEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 5 types, 761 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-KOU / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine


Mass: 334.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 738 / 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: 2.54 Å3/Da / Density % sol: 51.48 % / Description: Large plate-like crystal.
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 50mM Bicine-NaOH, pH 7.8, containing 9% PEG3350, 50mM NaCl, 2mM spermine
PH range: 7.6-8.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. all: 126505 / Num. obs: 126505 / % possible obs: 99.5 % / Redundancy: 5.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.039 / Rrim(I) all: 0.094 / Rsym value: 0.085 / Net I/σ(I): 9.9 / Num. measured all: 710786
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.632 / Num. measured all: 96459 / Num. unique obs: 18128 / CC1/2: 0.859 / Rpim(I) all: 0.018 / Rrim(I) all: 0.045 / Rsym value: 0.041 / Net I/σ(I) obs: 2.2 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
MOSFLM7.2.2data reduction
SCALA3.2.22data scaling
MOLREP11.6.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HN4

4hn4


Resolution: 1.45→28.94 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1828 / WRfactor Rwork: 0.1429 / FOM work R set: 0.8487 / SU B: 2.779 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0646 / SU Rfree: 0.0609 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1856 6241 4.9 %RANDOM
Rwork0.1469 ---
obs0.1488 120118 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.81 Å2 / Biso mean: 23.82 Å2 / Biso min: 8.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20.05 Å2
2--0.11 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 1.45→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4922 0 80 767 5769
Biso mean--43.27 37.78 -
Num. residues----650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125244
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.6447106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0525681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40122.124259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99715873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2621535
X-RAY DIFFRACTIONr_chiral_restr0.0910.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023965
X-RAY DIFFRACTIONr_rigid_bond_restr1.78835244
X-RAY DIFFRACTIONr_sphericity_free27.0235463
X-RAY DIFFRACTIONr_sphericity_bonded13.01855457
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 509 -
Rwork0.282 8577 -
all-9086 -
obs--97.58 %
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)
15.35761.07521.97690.338-0.31534.88840.2396-0.1172-0.14560.03140.01710.0010.2103-0.4172-0.25670.0188-0.01-0.00020.1173-0.01160.0993-59.667-21.55425.797
20.0564-0.08830.0550.327-0.49040.93210.07040.0510.0587-0.063-0.0683-0.0514-0.03430.0103-0.00210.09650.07460.06660.07670.01630.1196-41.559-12.1619.076
30.7057-0.7184-0.24560.94620.36770.19830.09190.0020.0216-0.0143-0.08010.0008-0.0016-0.0406-0.01180.0539-0.00650.02320.0809-0.01080.0646-41.664-24.09827.57
40.5082-0.17790.50521.6122-0.77420.8120.0980.0765-0.1225-0.09960.02760.11330.0774-0.0491-0.12560.04610.0656-0.04930.1546-0.0380.0781-52.122-32.29513.462
53.08352.0421.14892.03570.37110.68040.1030.05070.0262-0.0402-0.0590.0650.04710.0145-0.0440.10340.11820.03930.14020.04040.0584-48.787-13.259.411
64.58913.60011.90534.31381.41860.90610.00460.13770.3377-0.0623-0.08810.2349-0.0923-0.04540.08360.10710.11190.02340.14310.06480.1004-51.809-4.89512.807
70.85220.0345-0.52380.02970.02460.408-0.00460.0793-0.07890.029-0.0492-0.00230.0378-0.16070.05380.0474-0.026-0.01160.1645-0.01990.0363-30.482-42.63413.985
80.18340.0041-0.21040.12120.15470.4594-0.05170.0309-0.01650.01740.03390.01430.07260.04580.01780.0598-0.0039-0.01520.0901-0.0070.0461-3.965-47.115.706
90.0985-0.03710.07550.01730.0030.42130.01690.04670.0024-0.0075-0.0179-0.00540.0216-0.00030.00090.0573-0.0026-0.01120.0893-0.00750.0444-8.765-41.5035.789
100.12250.07640.13720.50870.17680.90060.07750.0229-0.032-0.04740.0405-0.0898-0.1793-0.139-0.1180.13340.0480.0220.10250.00950.0276-17.435-26.6330.82
110.07280.0994-0.20190.1519-0.33320.82610.0430.07860.01850.05060.0730.0353-0.042-0.1515-0.1160.06880.0431-0.00890.17940.02040.035-27.006-31.5437.907
120.22290.0051-0.03220.0280.07990.25090.0069-0.02040.0214-0.0006-0.00350.00830.01040.0019-0.00340.0562-0.0005-0.00370.0756-0.00060.0528-8.115-36.28720.313
130.2869-0.2423-0.19080.2885-0.0050.59120.1006-0.00970.0324-0.06970.03330.0067-0.08820.0686-0.13390.0717-0.01470.02330.1039-0.0290.03834.35-30.33315.503
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 13
2X-RAY DIFFRACTION2A14 - 77
3X-RAY DIFFRACTION3A78 - 159
4X-RAY DIFFRACTION4A160 - 216
5X-RAY DIFFRACTION5A217 - 247
6X-RAY DIFFRACTION6A248 - 267
7X-RAY DIFFRACTION7B2 - 37
8X-RAY DIFFRACTION8B38 - 70
9X-RAY DIFFRACTION9B71 - 100
10X-RAY DIFFRACTION10B101 - 165
11X-RAY DIFFRACTION11B166 - 196
12X-RAY DIFFRACTION12B197 - 364
13X-RAY DIFFRACTION13B365 - 396

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