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- PDB-6ub9: Crystal structure of tryptophan synthase from M. tuberculosis - A... -

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Basic information

Entry
Database: PDB / ID: 6ub9
TitleCrystal structure of tryptophan synthase from M. tuberculosis - AMINOACRYLATE- AND BRD6309-BOUND FORM
Components(Tryptophan synthase ...) x 2
KeywordsLyase/Lyase Inhibitor / PLP / heterotetramer / amino acid biosynthesis / substrate channeling / allostery / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Lyase-Lyase Inhibitor complex
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
ACETATE ION / : / FORMIC ACID / Chem-H9V / MALONIC ACID / Chem-P1T / TRIETHYLENE GLYCOL / Tryptophan synthase beta chain / Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.783 Å
AuthorsChang, C. / Michalska, K. / Maltseva, N.I. / Jedrzejczak, R. / McCarren, P. / Nag, P.P. / Joachimiak, A. / Satchell, K. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support Canada, 1items
OrganizationGrant numberCountry
Structure-guided Drug Discovery Coalition Canada
CitationJournal: To be Published
Title: Crystal structure of tryptophan synthase from M. tuberculosis - AMINOACRYLATE- AND BRD6309-BOUND FORM
Authors: Chang, C. / Michalska, K. / Maltseva, N.I. / Jedrzejczak, R. / McCarren, P. / Nag, P.P. / Joachimiak, A. / Satchell, K. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
SupersessionOct 30, 2019ID: 6DUA
Revision 1.1Oct 30, 2019Group: Advisory / Data collection / Category: pdbx_database_PDB_obs_spr
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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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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
C: Tryptophan synthase alpha chain
D: Tryptophan synthase beta chain
E: Tryptophan synthase alpha chain
F: Tryptophan synthase beta chain
G: Tryptophan synthase alpha chain
H: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,44044
Polymers287,6568
Non-polymers4,78436
Water3,099172
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)146,18922
Polymers143,8284
Non-polymers2,36118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11550 Å2
ΔGint-117 kcal/mol
Surface area41510 Å2
MethodPISA
2
E: Tryptophan synthase alpha chain
F: Tryptophan synthase beta chain
G: Tryptophan synthase alpha chain
H: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,25022
Polymers143,8284
Non-polymers2,42218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-121 kcal/mol
Surface area41400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.373, 159.619, 164.932
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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

#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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFY1, tryptophan synthase
#2: Protein
Tryptophan synthase beta chain


Mass: 43334.598 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: trpB, Rv1612, MTCY01B2.04 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFX9, tryptophan synthase

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Non-polymers , 9 types, 208 molecules

#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H4O4
#5: Chemical
ChemComp-P1T / 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID


Mass: 318.220 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15N2O7P
#6: Chemical
ChemComp-H9V / (2R,3S,4R)-3-(4'-chloro-2',6'-difluoro[1,1'-biphenyl]-4-yl)-4-(fluoromethyl)azetidine-2-carbonitrile


Mass: 336.739 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H12ClF3N2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cs
#8: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 8% TACSIMATE, 20% PEG3350, 5% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.783→30 Å / Num. obs: 84351 / % possible obs: 94.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.086 / Rrim(I) all: 0.219 / Χ2: 0.935 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.855.31.29640720.5890.5791.4250.74892.3
2.85-2.95.41.21740790.6140.5391.3350.79692.2
2.9-2.965.51.09640550.6630.4831.2010.77592.2
2.96-3.025.70.97840910.7390.4281.070.77692.1
3.02-3.085.70.84340580.7880.3680.9220.80192
3.08-3.155.80.68340750.8290.2970.7470.82992.2
3.15-3.235.90.56740400.8720.2440.6190.81991.5
3.23-3.3260.47940560.9020.2060.5230.85291.5
3.32-3.426.10.38540450.920.1650.420.88191.7
3.42-3.536.20.33840440.9410.1440.3680.89291.3
3.53-3.656.30.26240600.9650.110.2850.91791.4
3.65-3.86.30.2240670.9770.0920.2390.92391.7
3.8-3.976.30.18241510.9860.0760.1970.96592.8
3.97-4.186.20.15742590.9890.0650.170.96695.7
4.18-4.446.20.12643960.9930.0530.1371.08698.4
4.44-4.786.30.10544710.9950.0440.1141.11499.8
4.78-5.266.30.10845020.9950.0450.1171.03399.9
5.26-6.026.30.11645190.9940.0490.1260.897100
6.02-7.566.40.0845750.9960.0340.0870.93499.8
7.56-306.20.03947360.9950.0170.0431.45699.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TCJ

5tcj


Resolution: 2.783→29.893 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.85
RfactorNum. reflection% reflection
Rfree0.2097 1675 1.99 %
Rwork0.1687 --
obs0.1695 84265 93.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.03 Å2 / Biso mean: 43.1215 Å2 / Biso min: 15.77 Å2
Refinement stepCycle: final / Resolution: 2.783→29.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19122 0 288 172 19582
Biso mean--49.79 32.77 -
Num. residues----2598
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7833-2.86520.30611380.2729606583
2.8652-2.95760.31791350.2655667792
2.9576-3.06320.28411290.2517670692
3.0632-3.18570.25531510.225665392
3.1857-3.33050.27651440.2076669191
3.3305-3.50580.25161360.1937663891
3.5058-3.72510.20311330.1627667791
3.7251-4.01210.18421470.151680993
4.0121-4.41470.1621460.1392715297
4.4147-5.05080.1911260.12967388100
5.0508-6.35340.19371620.15377465100
6.3534-29.8930.14541280.13227669100
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)
10.6238-0.0512-0.38510.984-0.17451.8194-0.05340.0665-0.1179-0.1718-0.0698-0.00080.26360.01010.11530.2569-0.00090.01870.2108-0.03360.247731.6617-24.2556-12.7953
22.22770.09920.34421.7491-0.68942.00910.1323-0.1015-0.2196-0.02320.00960.5220.0807-0.1739-0.13290.23720.03840.02790.2885-0.04630.4736-18.111713.561414.7069
30.8105-0.1164-0.45771.02530.20921.29160.0431-0.0330.0247-0.0667-0.040.0957-0.0853-0.0329-0.00580.2157-0.0052-0.02120.2542-0.01090.252516.36593.7132.6742
42.704-0.66850.60721.117-0.00782.46780.08640.365-0.0738-0.0945-0.1184-0.29610.11790.24150.0350.24380.0080.06140.35590.04380.463586.4661-12.797316.7208
50.71420.1008-0.39150.97130.10241.19740.0438-0.0508-0.0180.0243-0.0252-0.1022-0.09260.0937-0.02250.21860.0003-0.00870.27470.0310.246451.3885-5.01828.5037
61.493-0.80160.26052.6723-0.63612.0479-0.0193-0.34870.02740.8740.02810.3146-0.4428-0.2424-0.00550.6033-0.08640.16680.3826-0.0090.40379.3326-26.804578.2186
70.77230.1812-0.39470.71360.09381.36580.02-0.0455-0.03090.0265-0.0705-0.01040.0743-0.11120.05250.2057-0.00590.00130.27580.02440.272224.3111-21.839443.8359
81.76180.72320.14831.1660.56711.7563-0.65460.7152-0.2222-1.00080.429-0.33610.30890.20770.17231.0535-0.18680.24310.608-0.08750.476841.5056-35.9345-47.2182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'F' and resid 8 through 407)F8 - 407
2X-RAY DIFFRACTION2(chain 'G' and resid 9 through 267)G9 - 267
3X-RAY DIFFRACTION3(chain 'H' and resid 5 through 407)H5 - 407
4X-RAY DIFFRACTION4(chain 'A' and resid 8 through 267)A8 - 267
5X-RAY DIFFRACTION5(chain 'B' and resid 5 through 408)B5 - 408
6X-RAY DIFFRACTION6(chain 'C' and resid 8 through 266)C8 - 266
7X-RAY DIFFRACTION7(chain 'D' and resid 9 through 407)D9 - 407
8X-RAY DIFFRACTION8(chain 'E' and resid 9 through 266)E9 - 266

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