[English] 日本語
Yorodumi
- PDB-1cj0: CRYSTAL STRUCTURE OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cj0
TitleCRYSTAL STRUCTURE OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE AT 2.8 ANGSTROM RESOLUTION
ComponentsPROTEIN (SERINE HYDROXYMETHYLTRANSFERASE)
KeywordsTRANSFERASE / HYDROXYMETHYL TRANSFERASE / 1 CARBON METABOLISM
Function / homology
Function and homology information


cellular response to tetrahydrofolate / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process ...cellular response to tetrahydrofolate / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / mRNA regulatory element binding translation repressor activity / cellular response to leukemia inhibitory factor / mRNA 5'-UTR binding / pyridoxal phosphate binding / protein homotetramerization / protein homodimerization activity / zinc ion binding / nucleoplasm / cytosol
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 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (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 1 / Aspartate Aminotransferase, domain 1 / 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 / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Serine hydroxymethyltransferase, cytosolic
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.8 Å
AuthorsScarsdale, J.N. / Kazanina, G. / Radaev, S. / Schirch, V. / Wright, H.T.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal structure of rabbit cytosolic serine hydroxymethyltransferase at 2.8 A resolution: mechanistic implications.
Authors: Scarsdale, J.N. / Kazanina, G. / Radaev, S. / Schirch, V. / Wright, H.T.
History
DepositionApr 20, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 6, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: PROTEIN (SERINE HYDROXYMETHYLTRANSFERASE)
B: PROTEIN (SERINE HYDROXYMETHYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9084
Polymers103,4142
Non-polymers4942
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.380, 116.380, 165.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.172468, -0.82198, 0.542773), (-0.835046, -0.170255, -0.523174), (0.522448, -0.543471, -0.657028)
Vector: 72.9841, 160.2029, 135.9227)

-
Components

#1: Protein PROTEIN (SERINE HYDROXYMETHYLTRANSFERASE) / SHMT


Mass: 51706.785 Da / Num. of mol.: 2 / Mutation: N5Q
Source method: isolated from a genetically manipulated source
Details: EACH PROTEIN MOLECULE HAS COVALENTLY LINKED PLP COFACTOR
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Strain: NEW ZEALAND WHITE / Cellular location: CYTOPLASM / Organ: LIVER / Plasmid: PET 22B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P07511
#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.: 12 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNO ELECTRON DENSITY WAS OBSERVED FOR THE FIRST 13 RESIDUES. IN CASES WHERE NO SIDECHAIN ELECTRON ...NO ELECTRON DENSITY WAS OBSERVED FOR THE FIRST 13 RESIDUES. IN CASES WHERE NO SIDECHAIN ELECTRON DENSITY WAS OBSERVED, RESIDUES WERE MODELED AS ALA DURING THE REFINEMENT AND ITERATIVE REBUILDING. IN ACCORDANCE WITH RCSB DIRECTIVES, SUCH RESIDUES HAVE BEEN ASSIGNED RESIDUE TYPES BASED ON THE EXPECTED SEQUENCE FOR RABBIT LIVER CYTOSILIC SHMT (SWS ENTRY P07511); HOWEVER COORDINATES ARE NOT INCLUDED FOR SIDECHAIN ATOMS BEYOND CB. THESE RESIDUES INCLUDE: MODEL SEQUENCE SWS P07511 SEQUENCE HIS A -5 HIS 17 LYS A 7 LYS 26 LYS A 20 LYS 37 GLN A 62 GLN 79 GLU A 69 GLU 86 LYS A 80 LYS 97 GLN A 892 GLN 108 LYS A 1341 LYS 156 LYS A 1342 LYS 157 LYS A 277 LYS 316 LYS A 354 LYS 392 SER A 355 SER 393 LYS A 375 LYS 415 PRO A 3962 PRO 440 ARG A 3963 ARG 441 LYS A 3991 LYS 445 LYS A 3994 LYS 448 LYS A 401 LYS 450 LYS A 405 LYS 456 ARG A 407 ARG 459 ARG A 410 ARG 462 GLN A 413 GLN 466 LEU A 4181 LEU 474 TRP B -8 TRP 14 HIS B -5 HIS 17 LYS B 7 LYS 26 LYS B 20 LYS 37 ARG B 41 ARG 58 LYS B 1341 LYS 156 LYS B 168 LYS 195 VAL B 2441 VAL 272 SER B 2443 SER 274 VAL B 2444 VAL 275 LYS B 245 LYS 281 ILE B 283 ILE 283 LYS B 354 LYS 393 SER B 355 SER 394 LEU B 357 LEU 396 ARG B 358 ARG 397 LYS B 380 LYS 419 ARG B 3963 ARG 441 LYS B 3991 LYS 445 LYS B 3994 LYS 448 GLU B 400 GLU 449 LYS B 401 LYS 450 LYS B 405 LYS 456 ARG B 407 ARG 459 GLN B 413 GLN 466

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 57 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: 20MM K2HPO4, KH2PO4, 25MM POTASIUM MES OR SODIUM HEPES, PH 7.0 0.2 MM 2-MERCAPTOETHANOL, 3% PEG 400, pH 6.0, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mM11K2HPO4/KH2/PO4
225 mMKMES11or sodium HEPES
30.2 mMEDTA11
45 mM2-mercaptoethanol11
53 %PEG400011

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→35 Å / Num. obs: 28327 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 19 % / Biso Wilson estimate: 88.8 Å2 / Rmerge(I) obs: 0.173 / Net I/σ(I): 10.9
Reflection shell
*PLUS
Mean I/σ(I) obs: 1

-
Processing

Software
NameVersionClassification
PHASESphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 2580178.46 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
Details: PROTEIN+PLP REFINED WITH TORSION ANGLE DYNAMICS, WATERS HELD FIXED. WATERS REFINED WITH CARTESIAN DYNAMICS, PROTEIN + PLP HELD FIXED. POSITIONAL NCS RESTRAINTS APPLIED BETWEEN EQUIVALENT ...Details: PROTEIN+PLP REFINED WITH TORSION ANGLE DYNAMICS, WATERS HELD FIXED. WATERS REFINED WITH CARTESIAN DYNAMICS, PROTEIN + PLP HELD FIXED. POSITIONAL NCS RESTRAINTS APPLIED BETWEEN EQUIVALENT RESIDUES IN CHAINS A + B. RESIDUES 9992- 1, 244-247, 4181-4180 AND 2291 WERE NOT RESTRAINED
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2885 10.1 %RANDOM
Rwork0.214 ---
obs-28454 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.08 Å2 / ksol: 0.236 e/Å3
Displacement parametersBiso mean: 70.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.65 Å20 Å20 Å2
2---2.65 Å20 Å2
3---5.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6982 0 30 12 7024
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINED / Rms dev position: 0.108 Å / Weight position: 150
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.442 446 9.6 %
Rwork0.399 4199 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMPLP.TOP
X-RAY DIFFRACTION3PLP.PARPATCH_PLP.TOP
X-RAY DIFFRACTION4PATCH_PLP.PARWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.17

+
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