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- PDB-2c2g: Crystal structure of Threonine Synthase from Arabidopsis thaliana... -

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Basic information

Entry
Database: PDB / ID: 2c2g
TitleCrystal structure of Threonine Synthase from Arabidopsis thaliana in complex with its cofactor pyridoxal phosphate
ComponentsTHREONINE SYNTHASE
KeywordsLYASE / SYNTHASE / THREONINE BIOSYNTHESIS / PYRIDOXAL PHOSPHATE / AMINO-ACID BIOSYNTHESIS
Function / homology
Function and homology information


threonine synthase / threonine synthase activity / threonine biosynthetic process / chloroplast stroma / chloroplast / pyridoxal phosphate binding / plasma membrane
Similarity search - Function
Threonine synthase-like / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / : / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Threonine synthase 1, chloroplastic
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsMas-Droux, C. / Biou, V. / Dumas, R.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Allosteric Threonine Synthase: Reorganization of the Pyridoxal Phosphate Site Upon Asymmetric Activation Through S-Adenosylmethionine Binding to a Novel Site.
Authors: Mas-Droux, C. / Biou, V. / Dumas, R.
History
DepositionSep 29, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Dec 16, 2015Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THREONINE SYNTHASE
B: THREONINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,2654
Polymers106,7712
Non-polymers4942
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-62.4 kcal/mol
Surface area33680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.626, 61.014, 76.678
Angle α, β, γ (deg.)108.96, 102.00, 107.36
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 36 - 479 / Label seq-ID: 36 - 479

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

NCS oper: (Code: given
Matrix: (0.93402, -0.16235, 0.31818), (-0.16007, -0.98654, -0.03351), (0.31934, -0.01963, -0.94744)
Vector: -0.48029, -4.15744, -0.23353)

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Components

#1: Protein THREONINE SYNTHASE


Mass: 53385.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RESIDUE 163 IS A LYSINE BOUND TO PYRIDOXAL PHOSPHATE VIA A SCHIFF BASE
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET23D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9S7B5, 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.: 121 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHYDROLYSES O-PHOSPHO-L-HOMOSERINE INTO L-THREONINE AND PHOSPHATE. OTHER_DETAILS: RESIDUE 163 IS A ...HYDROLYSES O-PHOSPHO-L-HOMOSERINE INTO L-THREONINE AND PHOSPHATE. OTHER_DETAILS: RESIDUE 163 IS A LYSINE BOUND TO PYRIDOXAL PHOSPHATE VIA A SCHIFF BASE: 2-LYSINE(3-HYDROXY-2-METHYL-5- PHOSPHONOOXYMETHYL- PYRIDIN-4-YLMETHANE)

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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: 2.33 Å3/Da / Density % sol: 46.85 %
Crystal growpH: 6.5
Details: 1 M LICL, 13% (W/V) PEG 6000, 5 MM DTT, 0.1 M MES-KOH, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 20, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 25774 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 6.8
Reflection shellResolution: 2.61→2.75 Å / Redundancy: 2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.5 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E5X

1e5x


Resolution: 2.61→20.63 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.898 / SU B: 27.272 / SU ML: 0.28 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-10 AND 347-362 IN MONOMER A, AND RESIDUES 1-20 AND 347-362 IN MONOMER B ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1311 5.1 %RANDOM
Rwork0.187 ---
obs0.191 24429 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å21.89 Å20.74 Å2
2--0.29 Å2-0.8 Å2
3----2.08 Å2
Refinement stepCycle: LAST / Resolution: 2.61→20.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6864 0 30 121 7015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0227053
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7081.9569564
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.0465879
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.8924.039307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.134151164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.5531540
X-RAY DIFFRACTIONr_chiral_restr0.2030.21046
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.025348
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2710.23575
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3320.24916
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2332
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8851.54525
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55227064
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.30832971
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4514.52500
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 3331 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.40.5
2Bmedium positional0.40.5
1Amedium thermal12
2Bmedium thermal12
LS refinement shellResolution: 2.61→2.68 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.333 93
Rwork0.315 1707
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)
15.37840.47010.79414.1096-1.54985.8461-0.1378-0.3201-0.8663-0.04320.2871-0.24490.77720.2996-0.1493-0.1938-0.0166-0.0538-0.14270.0411-0.0828.8488-11.077618.9964
25.90430.3154-0.63685.5527-1.65826.0059-0.17780.58330.5196-0.11180.1221-0.5534-0.57240.63330.0557-0.136-0.03050.11640.09340.1276-0.072914.89394.1169-15.4305
36.35381.1452-0.85730.45350.17640.55890.057-0.7358-0.390.1095-0.0241-0.01730.2163-0.199-0.0329-0.1227-0.027-0.0759-0.12530.0847-0.0936-16.3916-14.225215.4187
43.4962-0.8299-0.35741.3756-0.64135.4605-0.01630.7850.2932-0.2484-0.0790.1576-0.3314-0.52240.0953-0.04370.0558-0.00480.06430.146-0.0622-8.751112.3584-19.709
52.6535-0.90251.24032.1141-0.72863.6179-0.0906-0.30830.43220.31750.0473-0.0557-0.8355-0.41130.0432-0.0648-0.01120.0214-0.2412-0.0388-0.089-2.528912.294412.0959
63.54591.126-0.60081.24840.01382.7179-0.00260.7654-0.3403-0.4497-0.0388-0.09830.3415-0.0870.0414-0.0030.07970.0196-0.092-0.0889-0.091-0.956-16.3139-12.7653
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 132
2X-RAY DIFFRACTION2B10 - 132
3X-RAY DIFFRACTION3A163 - 271
4X-RAY DIFFRACTION3B450 - 481
5X-RAY DIFFRACTION4B163 - 271
6X-RAY DIFFRACTION4A450 - 481
7X-RAY DIFFRACTION5A133 - 162
8X-RAY DIFFRACTION5A272 - 346
9X-RAY DIFFRACTION5A363 - 449
10X-RAY DIFFRACTION6B133 - 162
11X-RAY DIFFRACTION6B272 - 346
12X-RAY DIFFRACTION6B363 - 449

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