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- PDB-5ocw: Structure of Mycobacterium tuberculosis tryptophan synthase in sp... -

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Basic information

Entry
Database: PDB / ID: 5ocw
TitleStructure of Mycobacterium tuberculosis tryptophan synthase in space group F222
Components
  • Tryptophan synthase alpha chain
  • Tryptophan synthase beta chain
KeywordsELECTRON TRANSPORT / tryptophan synthesis Mycobacterium tuberculosis
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-tryptophan biosynthetic process / plasma membrane / 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 / 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-P1T / Tryptophan synthase beta chain / Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsFutterer, K. / Abrahams, K. / Cox, J.A.G. / Besra, G.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Sci Rep / Year: 2017
Title: Inhibiting mycobacterial tryptophan synthase by targeting the inter-subunit interface.
Authors: Abrahams, K.A. / Cox, J.A.G. / Futterer, K. / Rullas, J. / Ortega-Muro, F. / Loman, N.J. / Moynihan, P.J. / Perez-Herran, E. / Jimenez, E. / Esquivias, J. / Barros, D. / Ballell, L. / Alemparte, C. / Besra, G.S.
History
DepositionJul 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation
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 1.2Apr 25, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
I: Tryptophan synthase alpha chain
J: Tryptophan synthase beta chain
K: Tryptophan synthase alpha chain
L: Tryptophan synthase beta chain
M: Tryptophan synthase alpha chain
N: Tryptophan synthase beta chain
O: Tryptophan synthase alpha chain
P: Tryptophan synthase beta chain
Q: Tryptophan synthase alpha chain
R: Tryptophan synthase beta chain
S: Tryptophan synthase alpha chain
T: Tryptophan synthase beta chain
U: Tryptophan synthase alpha chain
V: Tryptophan synthase beta chain
W: Tryptophan synthase alpha chain
X: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)925,26836
Polymers921,45024
Non-polymers3,81912
Water00
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)154,2116
Polymers153,5754
Non-polymers6362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)154,2116
Polymers153,5754
Non-polymers6362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Tryptophan synthase alpha chain
J: Tryptophan synthase beta chain
K: Tryptophan synthase alpha chain
L: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,2116
Polymers153,5754
Non-polymers6362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: Tryptophan synthase alpha chain
N: Tryptophan synthase beta chain
O: Tryptophan synthase alpha chain
P: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,2116
Polymers153,5754
Non-polymers6362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
Q: Tryptophan synthase alpha chain
R: Tryptophan synthase beta chain
S: Tryptophan synthase alpha chain
T: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,2116
Polymers153,5754
Non-polymers6362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
U: Tryptophan synthase alpha chain
V: Tryptophan synthase beta chain
W: Tryptophan synthase alpha chain
X: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,2116
Polymers153,5754
Non-polymers6362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)426.050, 432.110, 434.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
51I
61K
71M
81O
91Q
101S
111U
121W
12B
22D
32F
42H
52J
62L
72N
82P
92R
102T
112V
122X

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 500
2111C1 - 500
3111E1 - 500
4111G1 - 500
5111I1 - 500
6111K1 - 500
7111M1 - 500
8111O1 - 500
9111Q1 - 500
10111S1 - 500
11111U1 - 500
12111W1 - 500
1121B1 - 500
2121D1 - 500
3121F1 - 500
4121H1 - 500
5121J1 - 500
6121L1 - 500
7121N1 - 500
8121P1 - 500
9121R1 - 500
10121T1 - 500
11121V1 - 500
12121X1 - 500

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.546485, -0.459675, 0.700038), (-0.433391, -0.560035, -0.706069), (0.716608, -0.689246, 0.106832)79.79886, -82.04746, -103.11391
3given(0.692707, -0.495881, 0.523698), (-0.720423, -0.509853, 0.470149), (0.033871, -0.70296, -0.710423)-72.88399, 75.81335, -113.61063
4given(-0.060852, -0.009523, -0.998101), (0.106757, 0.994156, -0.015994), (0.992421, -0.107528, -0.05948)8.42278, -16.94049, -221.22591
5given(-0.051427, -0.019848, -0.998479), (-0.997773, 0.043551, 0.050525), (0.042482, 0.998854, -0.022044)-1.75016, 3.85078, -3.88365
6given(0.492642, 0.722913, 0.484459), (0.571556, -0.688581, 0.446295), (0.656222, 0.057032, -0.752409)79.76565, -79.7285, -107.02471
7given(-0.049415, -0.998713, 0.011413), (-0.998221, 0.049002, -0.033972), (0.033369, -0.013071, -0.999358)2.70539, -4.37864, -219.34595
8given(0.472508, 0.494665, -0.729413), (0.584585, 0.443448, 0.679422), (0.659543, -0.747436, -0.079641)-77.85774, 67.90852, -122.26543
9given(0.068301, -0.997244, -0.028985), (-0.101634, -0.035857, 0.994175), (-0.992474, -0.064957, -0.103803)-5.30195, 5.19707, -9.52616
10given(-0.708036, 0.535372, -0.460502), (0.704982, 0.497965, -0.505006), (-0.041052, -0.682208, -0.730005)75.0106, -76.50985, -105.58438
11given(0.999552, 0.006345, -0.029264), (0.02927, -0.000895, 0.999571), (0.006316, -0.999979, -0.00108)0.55817, -0.62519, -216.66626
12given(-0.559756, -0.699258, -0.444648), (-0.450457, 0.70715, -0.545002), (0.695529, -0.104773, -0.710818)-71.45295, 70.79623, -125.81619
13given(1), (1), (1)
14given(-0.559305, -0.441335, 0.701713), (-0.449712, -0.549563, -0.704088), (0.696374, -0.709369, 0.1089)79.88052, -81.88417, -102.42246
15given(0.701768, -0.492781, 0.514478), (-0.71177, -0.515475, 0.477146), (0.030072, -0.701036, -0.712491)-73.82378, 74.60266, -113.36509
16given(-0.065131, -0.012332, -0.997801), (0.071461, 0.997299, -0.01699), (0.995315, -0.07241, -0.064074)8.64933, -12.83476, -219.81514
17given(-0.047904, -0.017871, -0.998692), (-0.998657, 0.020597, 0.047534), (0.01972, 0.999628, -0.018834)-1.42056, 1.16792, -2.30144
18given(0.478167, 0.722174, 0.499821), (0.559379, -0.689161, 0.4606), (0.67709, 0.059345, -0.733503)79.46761, -78.76512, -106.81199
19given(-0.037944, -0.999237, 0.009301), (-0.999193, 0.037816, -0.013536), (0.013174, -0.009807, -0.999865)1.52486, -2.19022, -218.19252
20given(0.462162, 0.508848, -0.726278), (0.569512, 0.457469, 0.682919), (0.679752, -0.729243, -0.078371)-77.39137, 68.85973, -121.61781
21given(0.071655, -0.997269, -0.017897), (-0.079426, -0.023591, 0.996562), (-0.994262, -0.069988, -0.0809)-5.03674, 3.37292, -8.10414
22given(-0.701315, 0.52165, -0.485838), (0.712648, 0.496805, -0.495296), (-0.017004, -0.69359, -0.720169)75.46553, -76.7848, -107.64538
23given(0.999629, -0.002236, -0.027132), (0.02713, -0.001094, 0.999631), (-0.002265, -0.999997, -0.001033)-0.24656, -0.54134, -216.44379
24given(-0.569723, -0.70088, -0.429165), (-0.462908, 0.705158, -0.537093), (0.679067, -0.107331, -0.726187)-71.90334, 70.77483, -125.70799

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Components

#1: Protein
Tryptophan synthase alpha chain


Mass: 29921.943 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: trpA, Rv1613, MTCY01B2.05 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFY1, tryptophan synthase
#2: Protein
Tryptophan synthase beta chain


Mass: 46865.520 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: trpB, Rv1612, MTCY01B2.04 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFX9, tryptophan synthase
#3: 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.: 12 / Source method: obtained synthetically / Formula: C11H15N2O7P

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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: 5.42 Å3/Da / Density % sol: 77.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, pH 6.0, 50 % polypropylene 701 glycol 400, 5 % DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 4→49.8 Å / Num. obs: 160634 / % possible obs: 96.3 % / Redundancy: 3.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.4
Reflection shellResolution: 4→4.07 Å / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.539

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E0K

5e0k


Resolution: 4→49.8 Å / Cor.coef. Fo:Fc: 0.815 / Cor.coef. Fo:Fc free: 0.788 / SU B: 222.14 / SU ML: 1.258 / Cross valid method: THROUGHOUT / ESU R Free: 0.913 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.36779 8243 5 %RANDOM
Rwork0.3578 ---
obs0.3583 156611 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 126.446 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å20 Å2
2---3.39 Å20 Å2
3---1.97 Å2
Refinement stepCycle: 1 / Resolution: 4→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms57314 0 252 0 57566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.01958974
X-RAY DIFFRACTIONr_bond_other_d0.0120.0256290
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.96480177
X-RAY DIFFRACTIONr_angle_other_deg2.5763128689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.61357801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03822.7882496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.576158861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.17615564
X-RAY DIFFRACTIONr_chiral_restr0.0790.28987
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02168833
X-RAY DIFFRACTIONr_gen_planes_other0.0050.0213603
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4→4.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 553 -
Rwork0.394 10507 -
obs--90.47 %
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)
11.5284-0.2894-0.24173.04310.93311.2839-0.46630.2518-0.0789-0.1420.22670.27630.32990.12290.23950.4441-0.04880.06570.71880.06240.052223.878-25.0167-76.6997
21.3831-0.1205-0.19951.0725-0.30641.05280.3634-0.0611-0.08390.2695-0.24790.0208-0.42470.1589-0.11550.86440.51280.13191.74660.52360.413140.584-22.4468-23.2603
31.54790.02840.5291.0539-0.34731.1582-0.50710.67020.94590.0033-0.0563-0.2241-0.28370.19050.56341.4092-0.8322-1.08341.73450.65181.413423.7056-75.5851-25.4115
42.17920.0120.88210.44370.22990.976-0.18520.4155-0.01650.09740.06920.15460.08090.12770.1161.1917-1.04710.20492.1531-0.11490.080623.7389-24.5906-140.7966
51.48730.1753-0.29790.8106-0.05031.11470.3232-0.0495-0.14470.3559-0.5041-0.1258-0.37960.23820.18091.08880.1477-0.46011.0806-0.00320.602572.5945-22.7623-22.9637
61.82210.10450.5040.97930.14152.3213-0.040.625-0.0759-0.28850.0308-0.0235-0.45660.29530.00920.36290.1804-0.0861.411-0.39180.947623.1655-139.8486-25.3154
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 267
2X-RAY DIFFRACTION1C8 - 266
3X-RAY DIFFRACTION1B9 - 407
4X-RAY DIFFRACTION1D9 - 407
5X-RAY DIFFRACTION2E8 - 267
6X-RAY DIFFRACTION2G8 - 266
7X-RAY DIFFRACTION2F9 - 407
8X-RAY DIFFRACTION2H9 - 407
9X-RAY DIFFRACTION3I8 - 267
10X-RAY DIFFRACTION3K8 - 266
11X-RAY DIFFRACTION3J9 - 407
12X-RAY DIFFRACTION3L9 - 407
13X-RAY DIFFRACTION4M8 - 267
14X-RAY DIFFRACTION4O8 - 266
15X-RAY DIFFRACTION4N9 - 407
16X-RAY DIFFRACTION4P9 - 407
17X-RAY DIFFRACTION5Q8 - 267
18X-RAY DIFFRACTION5S8 - 266
19X-RAY DIFFRACTION5R9 - 407
20X-RAY DIFFRACTION5T9 - 407
21X-RAY DIFFRACTION6U8 - 267
22X-RAY DIFFRACTION6W8 - 266
23X-RAY DIFFRACTION6V9 - 407
24X-RAY DIFFRACTION6X9 - 407

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