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- PDB-5tcf: Crystal structure of tryptophan synthase from M. tuberculosis - l... -

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Basic information

Entry
Database: PDB / ID: 5tcf
TitleCrystal structure of tryptophan synthase from M. tuberculosis - ligand-free form
Components(Tryptophan synthase ...) x 2
KeywordsLYASE / PLP / heterotetramer / amino acid biosynthesis / substrate channeling / allostery / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / plasma membrane / 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
FORMIC ACID / : / MALONATE ION / Tryptophan synthase beta chain / Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsMichalska, K. / Maltseva, N. / Jedrzejczak, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, Canada, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700058C United States
Structure-guided Drug Discovery Coalition Canada
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: A small-molecule allosteric inhibitor of Mycobacterium tuberculosis tryptophan synthase.
Authors: Wellington, S. / Nag, P.P. / Michalska, K. / Johnston, S.E. / Jedrzejczak, R.P. / Kaushik, V.K. / Clatworthy, A.E. / Siddiqi, N. / McCarren, P. / Bajrami, B. / Maltseva, N.I. / Combs, S. / ...Authors: Wellington, S. / Nag, P.P. / Michalska, K. / Johnston, S.E. / Jedrzejczak, R.P. / Kaushik, V.K. / Clatworthy, A.E. / Siddiqi, N. / McCarren, P. / Bajrami, B. / Maltseva, N.I. / Combs, S. / Fisher, S.L. / Joachimiak, A. / Schreiber, S.L. / Hung, D.T.
History
DepositionSep 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Apr 13, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / 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_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.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.ptnr2_label_seq_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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
G: Tryptophan synthase alpha chain
H: Tryptophan synthase beta chain
E: Tryptophan synthase alpha chain
F: Tryptophan synthase beta chain
C: Tryptophan synthase alpha chain
D: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,06136
Polymers288,5698
Non-polymers1,49228
Water8,377465
1
A: Tryptophan synthase alpha chain
B: Tryptophan synthase beta chain
C: Tryptophan synthase alpha chain
D: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,16521
Polymers144,2844
Non-polymers88117
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11810 Å2
ΔGint-19 kcal/mol
Surface area43730 Å2
MethodPISA
2
G: Tryptophan synthase alpha chain
H: Tryptophan synthase beta chain
E: Tryptophan synthase alpha chain
F: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,89615
Polymers144,2844
Non-polymers61111
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-21 kcal/mol
Surface area43530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.137, 157.989, 166.651
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Tryptophan synthase ... , 2 types, 8 molecules AGECBHFD

#1: Protein
Tryptophan synthase alpha chain


Mass: 28579.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: trpA, Rv1613, MTCY01B2.05 / Plasmid: pMCSG81, pMCSG81-pRSF
Details (production host): pMCSG81 coexpresses TrpA with TrpB, pMCSG81-pRSF provides additional copy of TrpA
Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: P9WFY1, tryptophan synthase
#2: Protein
Tryptophan synthase beta chain


Mass: 43562.711 Da / Num. of mol.: 4 / Fragment: UNP 13-422
Source method: isolated from a genetically manipulated source
Details: Lys101 is attached to PLP
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: trpB, Rv1612, MTCY01B2.04 / Plasmid: pMCSG81 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: P9WFX9, tryptophan synthase

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Non-polymers , 4 types, 493 molecules

#3: Chemical
ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical...
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 3.08 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 8% tacsimate pH 8.0, 20% PEG3350, 100 mM KCl, cryo 17% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 19, 2015 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 128446 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 16.36
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 2.03 / CC1/2: 0.703 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KFJ

1kfj


Resolution: 2.46→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 13.9 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20734 2493 1.9 %RANDOM
Rwork0.17578 ---
obs0.17639 125834 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--1.88 Å20 Å2
3----1.95 Å2
Refinement stepCycle: 1 / Resolution: 2.46→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19187 0 94 465 19746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01919718
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218776
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.95826759
X-RAY DIFFRACTIONr_angle_other_deg0.965342937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01352601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30122.861832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.269152927
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.83415184
X-RAY DIFFRACTIONr_chiral_restr0.0760.23000
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02122956
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024536
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8182.52210419
X-RAY DIFFRACTIONr_mcbond_other0.8182.52310420
X-RAY DIFFRACTIONr_mcangle_it1.4133.77913015
X-RAY DIFFRACTIONr_mcangle_other1.4133.77913016
X-RAY DIFFRACTIONr_scbond_it0.9822.6689299
X-RAY DIFFRACTIONr_scbond_other0.9662.6539255
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6453.93713745
X-RAY DIFFRACTIONr_long_range_B_refined3.12129.97721058
X-RAY DIFFRACTIONr_long_range_B_other3.12329.98121059
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.461→2.524 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 133 -
Rwork0.258 8272 -
obs--89.37 %
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)
13.0155-1.14370.44721.9040.41781.57290.08960.18660.0931-0.1662-0.0358-0.32790.08540.0915-0.05380.0599-0.03710.09770.1519-0.00490.268385.7113-12.606117.2911
20.8110.0024-0.51031.20160.49621.32210.0247-0.00430.0174-0.06020.0082-0.1777-0.02770.1707-0.03290.0211-0.01050.01420.05060.0180.049250.593-5.840329.5149
32.46720.2295-0.23171.6713-0.48961.78360.0359-0.0425-0.17620.0733-0.0550.38580.0905-0.21410.01910.0470.00140.06120.121-0.06810.2557-18.560913.111915.0379
40.71240.0744-0.65281.1684-0.0871.28610.0378-0.00850.05670.0389-0.02280.1648-0.0988-0.144-0.0150.0170.0010.01070.0516-0.02280.041315.86812.73433.4139
53.12510.85970.75951.43960.08992.3184-0.27960.8339-0.0477-0.80470.2452-0.27840.04270.40690.03440.623-0.05350.23250.5299-0.15820.306942.4212-36.174-46.3759
60.61620.1391-0.47011.3104-0.39541.6228-0.00090.0976-0.1233-0.1536-0.0387-0.09520.25190.08110.03960.06720.02410.0080.0426-0.03530.047631.5097-24.2844-11.8668
71.5636-0.87750.07562.9762-0.10012.0489-0.0598-0.27120.1970.5714-0.01070.0283-0.3414-0.18860.07050.2551-0.04040.08180.164-0.00160.19589.1919-26.731979.6813
80.7270.1464-0.4040.8790.47371.6548-0.008-0.0815-0.09710.0723-0.02180.08120.1355-0.09610.02980.0305-0.02970.00060.04930.02740.04624.1456-22.160844.997
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 267
2X-RAY DIFFRACTION2B5 - 409
3X-RAY DIFFRACTION3G9 - 266
4X-RAY DIFFRACTION4H4 - 408
5X-RAY DIFFRACTION5E9 - 265
6X-RAY DIFFRACTION6F9 - 407
7X-RAY DIFFRACTION7C8 - 265
8X-RAY DIFFRACTION8D10 - 407

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