[English] 日本語
Yorodumi
- PDB-1b3r: RAT LIVER S-ADENOSYLHOMOCYSTEIN HYDROLASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b3r
TitleRAT LIVER S-ADENOSYLHOMOCYSTEIN HYDROLASE
ComponentsPROTEIN (S-ADENOSYLHOMOCYSTEINE HYDROLASE)
KeywordsHYDROLASE / ADEONSYLHOMOCYSTEINE / ADOHCY / ADOHCYASE
Function / homology
Function and homology information


S-adenosylhomocysteine catabolic process / adenosylselenohomocysteinase activity / Sulfur amino acid metabolism / circadian sleep/wake cycle / adenyl nucleotide binding / chronic inflammatory response to antigenic stimulus / Methylation / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle ...S-adenosylhomocysteine catabolic process / adenosylselenohomocysteinase activity / Sulfur amino acid metabolism / circadian sleep/wake cycle / adenyl nucleotide binding / chronic inflammatory response to antigenic stimulus / Methylation / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / response to nutrient / NAD binding / melanosome / response to hypoxia / copper ion binding / endoplasmic reticulum / identical protein binding / nucleus / cytosol
Similarity search - Function
Adenosylhomocysteinase-like / Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain ...Adenosylhomocysteinase-like / Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHu, Y. / Komoto, J. / Huang, Y. / Takusagawa, F. / Gomi, T. / Ogawa, H. / Takata, Y. / Fujioka, M.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal structure of S-adenosylhomocysteine hydrolase from rat liver.
Authors: Hu, Y. / Komoto, J. / Huang, Y. / Gomi, T. / Ogawa, H. / Takata, Y. / Fujioka, M. / Takusagawa, F.
History
DepositionDec 14, 1998Processing site: RCSB
Revision 1.0Dec 23, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details / struct_conn

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (S-ADENOSYLHOMOCYSTEINE HYDROLASE)
B: PROTEIN (S-ADENOSYLHOMOCYSTEINE HYDROLASE)
C: PROTEIN (S-ADENOSYLHOMOCYSTEINE HYDROLASE)
D: PROTEIN (S-ADENOSYLHOMOCYSTEINE HYDROLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,5178
Polymers189,8634
Non-polymers2,6544
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23710 Å2
ΔGint-106 kcal/mol
Surface area56490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.760, 134.480, 102.260
Angle α, β, γ (deg.)90.00, 114.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999862, 0.014624, 0.007919), (-0.013128, -0.986364, 0.164057), (0.01021, 0.16393, 0.986419)47.2466, 0.4231, -0.2142
2given(-0.999882, 0.015133, -0.002566), (-0.014478, 0.985377, -0.169771), (0.005097, -0.169714, 0.98548)47.2856, 0.2216, -0.0268
3given(0.999979, 0.003426, -0.005466), (0.00341, -0.99999, -0.00282), (-0.005476, 0.002802, -0.999981)0.0135, 0.0856, 0.1867

-
Components

#1: Protein
PROTEIN (S-ADENOSYLHOMOCYSTEINE HYDROLASE)


Mass: 47465.711 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN (1 - 181 & 352 - 402)
Source method: isolated from a genetically manipulated source
Details: EACH SUBUNIT CONTAINS ONE NAD+ MOLECULE. / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: MV1304 / Organ: LIVER / Plasmid: PUC118 / Production host: Escherichia coli (E. coli) / Strain (production host): MV1304 / References: UniProt: P10760, adenosylhomocysteinase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 6.8
Details: 50 MM TRIS/HCL (PH 6.8), 6 MM MGCL2, 5% MPD, 15% PEG-6K
Components of the solutions
IDNameCrystal-IDSol-ID
150 MM TRIS/HCL (PH 6.8)12
26 MM MGCL212
315% PEG-6K12
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 26 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl1drop
210 mM1dropMgCl2
315 %(w/v)PEG60001drop
410 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 56314 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 10.1
Reflection shellResolution: 2.8→3 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.173 / % possible all: 98
Reflection
*PLUS
Num. measured all: 280288 / Rmerge(I) obs: 0.07

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
KUMDSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NAD-BINDING DOMAIN IN FORMATE DEHYDROGENASE

Resolution: 2.8→8 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: APPLIED / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 -5 %RANDOM SELECTION
Rwork0.199 ---
obs-56314 97.5 %-
Displacement parametersBiso mean: 21.5 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16088 0 208 1239 17535
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.74
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.8→2.92 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.362 -5 %
Rwork0.273 5843 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN-REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.NADTOPOLOGY.NAD
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.362 / % reflection Rfree: 5 % / Rfactor Rwork: 0.273

+
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