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- PDB-2d1f: Structure of Mycobacterium tuberculosis threonine synthase -

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Basic information

Entry
Database: PDB / ID: 2d1f
TitleStructure of Mycobacterium tuberculosis threonine synthase
ComponentsThreonine synthase
KeywordsLYASE / amino acid synthesis / PYRIDOXAL-5'-PHOSPHATE / PLP
Function / homology
Function and homology information


threonine synthase / threonine synthase activity / threonine biosynthetic process / pyridoxal phosphate binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Threonine synthase, bacterial/archaeal / Threonine synthase-like / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Threonine synthase / Threonine synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCovarrubias, A.S. / Bergfors, T. / Mannerstedt, K. / Oscarson, S. / Jones, T.A. / Mowbray, S.L. / Hogbom, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural, biochemical, and in vivo investigations of the threonine synthase from Mycobacterium tuberculosis.
Authors: Covarrubias, A.S. / Hogbom, M. / Bergfors, T. / Carroll, P. / Mannerstedt, K. / Oscarson, S. / Parish, T. / Jones, T.A. / Mowbray, S.L.
History
DepositionAug 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Threonine synthase
B: Threonine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2084
Polymers74,7132
Non-polymers4942
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-57 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.964, 55.964, 368.378
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLN / End label comp-ID: PLP / Refine code: 4 / Auth seq-ID: 10 - 500 / Label seq-ID: 10

Dom-IDAuth asym-IDLabel asym-ID
1AA - C
2BB - D

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Components

#1: Protein Threonine synthase


Mass: 37356.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P66902, UniProt: P9WG59*PLUS, threonine synthase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: NaAc, NaCl, PEG 3350, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 3, 2004
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 19700 / Num. obs: 19700 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.07 / Net I/σ(I): 13.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.347 / % possible all: 56.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.928 / SU B: 34.378 / SU ML: 0.358 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25617 1047 5 %RANDOM
Rwork0.18739 ---
all0.19091 19700 --
obs0.19091 19700 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.928 Å2
Baniso -1Baniso -2Baniso -3
1-2.94 Å21.47 Å20 Å2
2--2.94 Å20 Å2
3----4.41 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 30 54 5168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225216
X-RAY DIFFRACTIONr_angle_refined_deg1.331.9737126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0045696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.18224.667180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.75215802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6931524
X-RAY DIFFRACTIONr_chiral_restr0.0930.2846
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023890
X-RAY DIFFRACTIONr_nbd_refined0.220.22540
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23572
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2192
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.24
X-RAY DIFFRACTIONr_mcbond_it0.3621.53521
X-RAY DIFFRACTIONr_mcangle_it0.63525562
X-RAY DIFFRACTIONr_scbond_it0.94931877
X-RAY DIFFRACTIONr_scangle_it1.4914.51564
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2557 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.410.5
medium thermal0.382
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 50 -
Rwork0.316 836 -
obs--53.21 %
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)
14.139-1.90090.2784.45520.081915.51670.16040.60210.278-1.0402-0.0530.437-1.9003-1.1206-0.10740.86970.1976-0.00890.19970.04650.1239-10.16756.155-19.929
22.1948-0.3677-0.13872.99771.55166.65720.16560.2409-0.0957-0.10170.138-0.09530.63280.6005-0.30360.23870.2085-0.07350.1169-0.0913-0.073-2.55733.394-12.529
38.2687-1.2773-2.60332.69110.043310.31960.043-1.1289-0.00330.68850.02610.73010.6284-0.9549-0.06910.4605-0.10860.10710.47-0.05160.1549-18.29336.42218.99
41.72770.4326-0.26752.63011.81136.82510.2833-0.49180.1055-0.00680.2652-0.0653-0.58351.0902-0.54850.1772-0.05740.10330.3766-0.1764-0.04851.60551.84513.152
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA85 - 16485 - 164
2X-RAY DIFFRACTION1BB339 - 358339 - 358
3X-RAY DIFFRACTION2AA10 - 8410 - 84
4X-RAY DIFFRACTION2AA165 - 338165 - 338
5X-RAY DIFFRACTION3BB85 - 16485 - 164
6X-RAY DIFFRACTION3AA339 - 358339 - 358
7X-RAY DIFFRACTION4BB10 - 8410 - 84
8X-RAY DIFFRACTION4BB165 - 338165 - 338

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