[English] 日本語
Yorodumi
- PDB-2c2g: Crystal structure of Threonine Synthase from Arabidopsis thaliana... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more