[English] 日本語
Yorodumi
- PDB-6cd1: Crystal structure of Medicago truncatula serine hydroxymethyltran... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cd1
TitleCrystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3), complexes with reaction intermediates
Components(Serine hydroxymethyltransferase) x 2
KeywordsTRANSFERASE / PLP / one-carbon cycle / tetrahydrofolate / chloroplast / tetramer / PLP-Serine / PLP-Glycine
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / methyltransferase activity / pyridoxal phosphate binding / methylation / mitochondrion / cytoplasm
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / GLYCINE / Chem-PLG / Chem-PLS / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsRuszkowski, M. / Sekula, B. / Ruszkowska, A. / Dauter, Z.
CitationJournal: Front Plant Sci / Year: 2018
Title: Chloroplastic Serine Hydroxymethyltransferase FromMedicago truncatula: A Structural Characterization.
Authors: Ruszkowski, M. / Sekula, B. / Ruszkowska, A. / Dauter, Z.
History
DepositionFeb 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 4, 2023Group: 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
E: Serine hydroxymethyltransferase
F: Serine hydroxymethyltransferase
G: Serine hydroxymethyltransferase
H: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)399,50125
Polymers397,3928
Non-polymers2,10917
Water36,6062032
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,69913
Polymers198,3544
Non-polymers1,3459
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20190 Å2
ΔGint-92 kcal/mol
Surface area59610 Å2
MethodPISA
2
E: Serine hydroxymethyltransferase
F: Serine hydroxymethyltransferase
G: Serine hydroxymethyltransferase
H: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,80212
Polymers199,0384
Non-polymers7648
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19930 Å2
ΔGint-84 kcal/mol
Surface area59960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.086, 103.653, 180.379
Angle α, β, γ (deg.)90.00, 97.38, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 8 molecules ABCDFEGH

#1: Protein
Serine hydroxymethyltransferase


Mass: 49588.469 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11445860, MTR_2g018290 / Plasmid: pMCSG68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G7ILW0, glycine hydroxymethyltransferase
#2: Protein Serine hydroxymethyltransferase


Mass: 49816.586 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11445860, MTR_2g018290 / Plasmid: pMCSG68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G7ILW0, glycine hydroxymethyltransferase

-
Non-polymers , 6 types, 2049 molecules

#3: Chemical ChemComp-PLS / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE / PYRIDOXYL-SERINE-5-MONOPHOSPHATE


Mass: 336.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N2O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE


Mass: 306.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O7P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2032 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 75 mM MES pH 6.5, 19% PEG3350 and 150 mM ammonium acetate. The mature crystals were soaked with 200 mM Ser for 2 h and cryoprotected by the addition of ethylene glycol to a final concentration of 20%

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 263165 / % possible obs: 98.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.071 / Net I/σ(I): 13.3
Reflection shellResolution: 1.91→2.02 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 41826 / Rrim(I) all: 0.83 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ccz

6ccz


Resolution: 1.91→46.65 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 10.953 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1316 0.5 %RANDOM
Rwork0.191 ---
obs0.191 261832 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.906 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0 Å20.43 Å2
2--1.24 Å2-0 Å2
3----0.57 Å2
Refinement stepCycle: 1 / Resolution: 1.91→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27693 0 138 2032 29863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01928501
X-RAY DIFFRACTIONr_bond_other_d0.0020.0227474
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.94438555
X-RAY DIFFRACTIONr_angle_other_deg0.98363228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43253615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36923.8061235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.302154784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.19515184
X-RAY DIFFRACTIONr_chiral_restr0.0870.24274
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02132405
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026411
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_it1.1632.69214484
X-RAY DIFFRACTIONr_mcbond_other1.1632.69214480
X-RAY DIFFRACTIONr_mcangle_it1.8864.02918089
X-RAY DIFFRACTIONr_mcangle_other1.8864.02818088
X-RAY DIFFRACTIONr_scbond_it1.3222.90214017
X-RAY DIFFRACTIONr_scbond_other1.3222.90214017
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2274.27620467
X-RAY DIFFRACTIONr_long_range_B_refined5.18522.41333302
X-RAY DIFFRACTIONr_long_range_B_other5.18522.41433303
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.957 Å
RfactorNum. reflection% reflection
Rfree0.366 94 -
Rwork0.349 18654 -
obs--95.47 %
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)
10.5529-0.17890.08730.21890.09340.1929-0.02390.0504-0.02130.02520.04130.0037-0.0481-0.0342-0.01740.12420.00570.04490.1491-0.03260.08570.397934.431682.1563
20.70580.0224-0.10220.633-0.10560.1167-0.0615-0.0387-0.09510.14440.0637-0.1747-0.08210.0079-0.00220.10520.002-0.01860.1391-0.02960.115222.564416.82896.5781
30.4703-0.0150.03850.2110.08020.11850.01330.0527-0.08240.0489-0.0417-0.02660.03430.01910.02840.06590.01440.01040.2366-0.02090.059553.919120.959251.4359
40.5815-0.3315-0.10360.32570.19120.43380.12860.1633-0.0193-0.0053-0.16990.0495-0.0732-0.04960.04130.11510.0150.0140.2984-0.03310.011629.073235.030136.4603
50.28340.0675-0.06840.3496-0.03570.0414-0.0203-0.0033-0.04090.00540.0244-0.0251-0.03620.0036-0.00410.10210.02370.06610.22130.02480.062235.018986.27327.6298
60.3121-0.0206-0.20290.62130.20250.2686-0.03260.0874-0.0973-0.0746-0.02080.0774-0.0732-0.11810.05350.07850.02520.03060.2831-0.01490.051912.342869.2636-7.8058
70.5708-0.12310.11930.26850.04680.21590.0074-0.0319-0.0706-0.02430.00080.00150.0702-0.0619-0.00820.08760.02190.02680.20140.04170.059-18.601569.776536.7583
80.4562-0.24890.11740.5578-0.04090.1909-0.0603-0.07270.14040.06020.1022-0.1793-0.0131-0.0854-0.04180.09660.0759-0.0250.2071-0.03020.1036.0982.763853.1333
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A82 - 533
2X-RAY DIFFRACTION1A601
3X-RAY DIFFRACTION2B83 - 533
4X-RAY DIFFRACTION2B601
5X-RAY DIFFRACTION3C82 - 533
6X-RAY DIFFRACTION3C601 - 602
7X-RAY DIFFRACTION4D83 - 533
8X-RAY DIFFRACTION4D601
9X-RAY DIFFRACTION5E83 - 533
10X-RAY DIFFRACTION5E601
11X-RAY DIFFRACTION6F83 - 533
12X-RAY DIFFRACTION6F601
13X-RAY DIFFRACTION7G83 - 533
14X-RAY DIFFRACTION7H601
15X-RAY DIFFRACTION8H82 - 533
16X-RAY DIFFRACTION8H602

+
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