[English] 日本語
Yorodumi
- PDB-1ygp: PHOSPHORYLATED FORM OF YEAST GLYCOGEN PHOSPHORYLASE WITH PHOSPHAT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ygp
TitlePHOSPHORYLATED FORM OF YEAST GLYCOGEN PHOSPHORYLASE WITH PHOSPHATE BOUND IN THE ACTIVE SITE.
ComponentsYEAST GLYCOGEN PHOSPHORYLASE
KeywordsGLYCOSYLTRANSFERASE / YEAST / PHOSPHORYLATED FORM
Function / homology
Function and homology information


Glycogen breakdown (glycogenolysis) / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / Neutrophil degranulation / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Glycosyl transferase, family 35 / Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site. / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Glycogen phosphorylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsLin, K. / Rath, V.L. / Dai, S.C. / Fletterick, R.J. / Hwang, P.K.
Citation
Journal: Science / Year: 1996
Title: A protein phosphorylation switch at the conserved allosteric site in GP.
Authors: Lin, K. / Rath, V.L. / Dai, S.C. / Fletterick, R.J. / Hwang, P.K.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: Mechanism of Regulation in Yeast Glycogen Phosphorylase
Authors: Lin, K. / Hwang, P.K. / Fletterick, R.J.
#2: Journal: Nat.Struct.Biol. / Year: 1994
Title: Parallel Evolution in Two Homologues of Phosphorylase
Authors: Rath, V.L. / Fletterick, R.J.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Purification and Crystallization of Glycogen Phosphorylase from Saccharomyces Cerevisiae
Authors: Rath, V.L. / Hwang, P.K. / Fletterick, R.J.
History
DepositionMay 30, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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_ref_seq_dif / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: YEAST GLYCOGEN PHOSPHORYLASE
B: YEAST GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,4328
Polymers202,5582
Non-polymers8746
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8800 Å2
ΔGint-60 kcal/mol
Surface area59030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.910, 143.930, 169.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.756, 0.22, -0.617), (0.227, -0.927, -0.069), (-0.615, -0.088, -0.784)
Vector: 23.516, -197.668, -4.356)
DetailsTHE AUTHORS ONLY DEPOSITED ONE CHAIN. THE PDB GENERATED THE SECOND CHAIN IN THE ASYMMETRIC UNIT FROM THE CHAIN THAT WAS DEPOSITED USING THE TRANSFORMATION ON MTRIX RECORDS BELOW.

-
Components

#1: Protein YEAST GLYCOGEN PHOSPHORYLASE


Mass: 101278.820 Da / Num. of mol.: 2 / Mutation: N-TERMINAL 22 RESIDUE DELETION
Source method: isolated from a genetically manipulated source
Details: PHOSPHORYLATED FORM OF THE ENZYME
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YEAST GLYCOGEN PHOSPHORYLASE / Organ: TAIL / Plasmid: PTACTAC / Gene (production host): YEAST GLYCOGEN PHOSPHORYLASE / Production host: Escherichia coli (E. coli) / References: UniProt: P06738
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
Sequence detailsTHE NUMBERING OF RESIDUES IS RELATIVE TO THE MAMMALIAN GLYCOGEN PHOSPHORYLASE SEQUENCE. THE LONGER ...THE NUMBERING OF RESIDUES IS RELATIVE TO THE MAMMALIAN GLYCOGEN PHOSPHORYLASE SEQUENCE. THE LONGER N-TERMINAL TAIL RESIDUES OF THE YEAST ENZYME ARE NUMBERED 1N TO 39N TOWARDS THE N-TERMINUS. INSERTION RESIDUES RELATIVE TO THE MAMMALIAN ENZYME ARE NUMBERED AS THE PRECEDING RESIDUE NUMBER FOLLOWED BY AN ALPHABETIC CHARACTER, STARTING WITH C. DISCONTINUITY IN THE NUMBERING (BETWEEN 315 AND 324, 722 AND 726) INDICATES THAT THERE ARE GAPS IN THOSE REGIONS RELATIVE TO THE MAMMALIAN ENZYME. OTHER DISCONTINUITY IN NUMBERING OF RESIDUES INDICATES THAT THOSE MISSING RESIDUES ARE DISORDERED IN THE STRUCTURE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Details: used to seeding, Lin, K., (1997) Structure, 5, 1511.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
132 mg/mlprotein1drop
2130 mMsodium succinate1drop
32 mMDTT1drop
40.2 mMEDTA1drop
50.001 mg/mlleupeptin1drop
60.001 mg/mlaprotonin1drop
70.001 mg/mlpepstatin A1drop
80.5 mMPMSF1drop
90.02 %sodium azide1drop
10100 mMBis-Tris1reservoir
1150 mM1reservoirNaCl
1250 mMGlc-1-P1reservoir
13400 mMammonium sulfate1reservoir
144.5 %PEG40001reservoir
15reservoir1dropequal volume of drop solution

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 8, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 50707 / % possible obs: 72 % / Observed criterion σ(I): 1.5 / Redundancy: 5 % / Rmerge(I) obs: 0.105
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. measured all: 247322
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 3 Å / Redundancy: 0.043 %

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.8→6 Å / σ(F): 2
Details: RESIDUE PHE 750 IS AT THE BEGINNING OF A BROKEN LOOP FOR WHICH THE ELECTRON DENSITY IS POOR. IT HAS A BAD PHI/PSI ANGLE, AND SHOULD BE IGNORED.
RfactorNum. reflection
Rfree0.239 -
Rwork0.179 -
obs0.179 247322
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13488 0 50 0 13538
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg2.87
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARAM19X.PRO
X-RAY DIFFRACTION2

+
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://pdbjlvh1.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