[English] 日本語
Yorodumi
- PDB-1htp: REFINED STRUCTURES AT 2 ANGSTROMS AND 2.2 ANGSTROMS OF THE TWO FO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1htp
TitleREFINED STRUCTURES AT 2 ANGSTROMS AND 2.2 ANGSTROMS OF THE TWO FORMS OF THE H-PROTEIN, A LIPOAMIDE-CONTAINING PROTEIN OF THE GLYCINE DECARBOXYLASE COMPLEX
ComponentsH-PROTEIN
KeywordsOXIDOREDUCTASES(ACTING ON CH-NH2 DONOR)
Function / homology
Function and homology information


glycine cleavage complex / glycine decarboxylation via glycine cleavage system / mitochondrion
Similarity search - Function
Glycine cleavage system H-protein, subgroup / Glycine cleavage system H-protein / Glycine cleavage system H-protein/Simiate / Glycine cleavage H-protein / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif ...Glycine cleavage system H-protein, subgroup / Glycine cleavage system H-protein / Glycine cleavage system H-protein/Simiate / Glycine cleavage H-protein / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-OSS / Glycine cleavage system H protein, mitochondrial
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsPares, S. / Cohen-Addad, C.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: The lipoamide arm in the glycine decarboxylase complex is not freely swinging.
Authors: Cohen-Addad, C. / Pares, S. / Sieker, L. / Neuburger, M. / Douce, R.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: X-Ray Structure Determination at 2.6 Angstroms Resolution of a Lipoate-Containing Protein: The H-Protein of the Glycine Decarboxylase Complex from Pea Leaves
Authors: Pares, S. / Cohen-Addad, C. / Sieker, L. / Neuburger, M. / Douce, R.
History
DepositionJan 11, 1995Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: H-PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2762
Polymers13,9621
Non-polymers3141
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.340, 55.380, 33.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein H-PROTEIN


Mass: 13962.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea)
References: UniProt: P16048, glycine dehydrogenase (aminomethyl-transferring)
#2: Chemical ChemComp-OSS / 6-(HYDROXYETHYLDITHIO)-8-(AMINOMETHYLTHIO)OCTANOIC ACID


Mass: 313.500 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23NO3S3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPND H-PROTEIN CHARGED IN METHYLAMINE OF THE GLYCINE DECARBOXYLASE COMPLEX FROM PEA THE H-PROTEIN ...COMPND H-PROTEIN CHARGED IN METHYLAMINE OF THE GLYCINE DECARBOXYLASE COMPLEX FROM PEA THE H-PROTEIN PROVIDES THE ATTACHMENT SITE FOR THE LIPOIC ACID VIA AN AMIDE LINKAGE TO THE EPSILON-AMINO GROUP OF A LYS63.
Sequence detailsSEQUENCE REFERENCE DATABASE: SWISS-PROT ENTRY_NAME: GCSH_PEA REFERENCE: MACHEREL D., LEBRUN M. ...SEQUENCE REFERENCE DATABASE: SWISS-PROT ENTRY_NAME: GCSH_PEA REFERENCE: MACHEREL D., LEBRUN M.,GAGNON J., NEUBURGER M., DOUCE R. BIOCHEM J. 268:783-789(1990) KIM Y., OLIVER D.J J. BIOL. CHEM. 265: 848-853(1990).

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal grow
*PLUS
Temperature: 8 ℃ / pH: 5.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17-14 mg/mlH-Proox1dropcan be replaced with 3-5mg/ml H-ProMet
20.1 MTrisMaleate1drop
32 Mammonium sulfate1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 5684 / % possible obs: 91 %
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 14236 / Rmerge(I) obs: 0.054

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.185 --
obs0.185 5457 90 %
Displacement parametersBiso mean: 17.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1180 0 17 145 1342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.1
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

+
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