[English] 日本語
Yorodumi
- PDB-6dk3: HUMAN MITOCHONDRIAL SERINE HYDROXYMETHYLTRANSFERASe 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dk3
TitleHUMAN MITOCHONDRIAL SERINE HYDROXYMETHYLTRANSFERASe 2
ComponentsSerine hydroxymethyltransferase, mitochondrial
KeywordsTRANSFERASE / SHMT2 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / L-serine biosynthetic process / serine binding / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity ...BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / L-serine biosynthetic process / serine binding / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / L-serine catabolic process / Metabolism of folate and pterines / regulation of oxidative phosphorylation / tetrahydrofolate metabolic process / response to type I interferon / protein K63-linked deubiquitination / tetrahydrofolate interconversion / regulation of aerobic respiration / mitochondrial nucleoid / folic acid metabolic process / RHOG GTPase cycle / mRNA regulatory element binding translation repressor activity / protein tetramerization / mRNA 5'-UTR binding / microtubule cytoskeleton / pyridoxal phosphate binding / one-carbon metabolic process / protein homotetramerization / mitochondrial inner membrane / mitochondrial matrix / chromatin binding / positive regulation of cell population proliferation / protein homodimerization activity / mitochondrion / extracellular exosome / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Serine hydroxymethyltransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.04 Å
AuthorsDong, A. / Wu, H. / Zeng, H. / Loppnau, P. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: HUMAN MITOCHONDRIAL SERINE HYDROXYMETHYLTRANSFERASe 2
Authors: Wu, H. / Dong, A. / Zeng, H. / Loppnau, P. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
History
DepositionMay 28, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionJun 20, 2018ID: 3OU5
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine hydroxymethyltransferase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)54,1127
Polymers54,1121
Non-polymers06
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19410 Å2
2
A: Serine hydroxymethyltransferase, mitochondrial

A: Serine hydroxymethyltransferase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)108,22314
Polymers108,2232
Non-polymers012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4920 Å2
ΔGint-23 kcal/mol
Surface area33900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.034, 75.029, 75.199
Angle α, β, γ (deg.)90.000, 108.770, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1251-

HOH

-
Components

#1: Protein Serine hydroxymethyltransferase, mitochondrial / / SHMT / Glycine hydroxymethyltransferase / Serine methylase


Mass: 54111.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT2 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P34897, glycine hydroxymethyltransferase
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 5% PEG 8000, 0.1 M Tris-HCL pH8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.912386 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912386 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 31273 / % possible obs: 98.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Χ2: 1.354 / Net I/σ(I): 14.3 / Num. measured all: 109928
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.04-2.083.30.39715220.754196.5
2.08-2.113.50.39215050.801197.7
2.11-2.153.60.31716010.854198.7
2.15-2.23.60.30315620.859199.2
2.2-2.253.70.23715460.932199.2
2.25-2.33.70.21515680.934199.4
2.3-2.353.60.18615550.988199.4
2.35-2.423.70.16316081.021199.6
2.42-2.493.60.14715621.152199.6
2.49-2.573.60.12515521.233199.4
2.57-2.663.70.10915851.245199.7
2.66-2.773.60.08915781.42199.3
2.77-2.893.60.0815841.593199.2
2.89-3.053.50.0715551.835199.4
3.05-3.243.60.05915761.814198.7
3.24-3.493.50.05315672.013198.2
3.49-3.843.40.04715471.991197.9
3.84-4.393.30.04315692.309197.5
4.39-5.543.20.04515641.776197.4
5.54-503.10.04215671.861195.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LS3

1ls3


Resolution: 2.04→33.56 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.363 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 641 2 %RANDOM
Rwork0.197 ---
obs0.1983 30632 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.04 Å2 / Biso mean: 45.721 Å2 / Biso min: 28.21 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å20 Å21.01 Å2
2---0.03 Å20 Å2
3---1.55 Å2
Refinement stepCycle: final / Resolution: 2.04→33.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3205 0 6 167 3378
Biso mean--30 50.6 -
Num. residues----423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0143272
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172899
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.6594430
X-RAY DIFFRACTIONr_angle_other_deg0.9641.6326787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.585421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06520.615179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70115534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2981533
X-RAY DIFFRACTIONr_chiral_restr0.0660.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023767
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02585
LS refinement shellResolution: 2.043→2.096 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 38 -
Rwork0.285 2156 -
all-2194 -
obs--93.8 %

+
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