[English] 日本語
Yorodumi
- PDB-2c4m: Starch phosphorylase: structural studies explain oxyanion-depende... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2c4m
TitleStarch phosphorylase: structural studies explain oxyanion-dependent kinetic stability and regulatory control.
ComponentsGLYCOGEN PHOSPHORYLASE
KeywordsTRANSFERASE / ALLOSTERIC CONTROL / PHOSPHATE DEPENDENCE / STARCH DEGRADING / PHOSPHORYLASE / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / pyridoxal phosphate binding / carbohydrate metabolic process
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
FORMIC ACID / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Alpha-1,4 glucan phosphorylase
Similarity search - Component
Biological speciesCORYNEBACTERIUM CALLUNAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPurvis, A. / Nidetzky, B. / Watson, K.
CitationJournal: To be Published
Title: Starch Phosphorylase: Structural Studies Explain Oxyanion-Dependent Kinetic Stability and Regulatory Control
Authors: Purvis, A. / Nidetzky, B. / Watson, K.
History
DepositionOct 20, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLYCOGEN PHOSPHORYLASE
B: GLYCOGEN PHOSPHORYLASE
C: GLYCOGEN PHOSPHORYLASE
D: GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)365,55639
Polymers362,6524
Non-polymers2,90435
Water20,7891154
1
A: GLYCOGEN PHOSPHORYLASE
B: GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,92522
Polymers181,3262
Non-polymers1,60020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: GLYCOGEN PHOSPHORYLASE
D: GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,63017
Polymers181,3262
Non-polymers1,30415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)99.266, 187.620, 129.315
Angle α, β, γ (deg.)90.00, 112.48, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
GLYCOGEN PHOSPHORYLASE / / STARCH PHOSPHORYLASE


Mass: 90662.922 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: PLP (1634) COFACTOR IS COVALENTLY LINKED TO LYS634 VIA SCHIFF BASE (C4A-NZ)
Source: (gene. exp.) CORYNEBACTERIUM CALLUNAE (bacteria) / Plasmid: PQE 30 / Production host: Escherichia coli DH5[alpha] (bacteria) / Variant (production host): XL1 BLUE / References: UniProt: Q8KQ56, glycogen phosphorylase

-
Non-polymers , 5 types, 1189 molecules

#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1154 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 225 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 225 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, SER 225 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 225 TO ALA ENGINEERED RESIDUE IN CHAIN C, SER 225 TO ALA ENGINEERED RESIDUE IN CHAIN D, SER 225 TO ALA THE ENGINEERED RESIDUE IN THE COORDINATES IS NUMBERED 224.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60 %
Description: TWO SCANS WERE PERFORMED ON THE SAME CRYSTAL AT HIGH 1.9 ANG AND LOW 2.5 ANG RESOLUTION
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: HANGING DROP VAPOUR DIFFUSION 8.4MG/ML PROTEIN SOLUTION, 0.1M SODIUM ACETATE PH 5.0, 8% PEG 8,000, 0.2M SODIUM FORMATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 16, 2003
Details: SAGITALLY FOCUSING GE (220) CRYSTAL AND BENT MULTILAYER
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 306185 / % possible obs: 89.7 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.1 / % possible all: 75.9

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GPA

1gpa


Resolution: 1.9→30 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3314122.3 / Isotropic thermal model: RESTRAINED / σ(F): 0
Details: INITIAL REFINEMENT WAS CARRIED OUT USING 4 FOLD NCS RESTRAINTS. IN THE REFINEMENT THE FOLLOWING RESIDUES WERE GIVEN ZERO OCCUPANCY DUE TO THE ABSENCE OF ELECTRON DENSITY. CHAIN ID A Q5, R43, ...Details: INITIAL REFINEMENT WAS CARRIED OUT USING 4 FOLD NCS RESTRAINTS. IN THE REFINEMENT THE FOLLOWING RESIDUES WERE GIVEN ZERO OCCUPANCY DUE TO THE ABSENCE OF ELECTRON DENSITY. CHAIN ID A Q5, R43, K281, E319, K327, V336, L337, E339, E378, E505, E510, D647, E659, K724, R775, R778. CHAIN ID B K281, E319, E339, E378, E501, E505, E510, E659, E677, N707, K724, E741, R775, R778. CHAIN ID C Q5, R92, E151, K281, D296, E339, E378, K474, K482, E505, R523, E546, D551, K724, K794. CHAIN ID D Q5, R43, E86, R92, E97, E151, K281, E319, E339, E378, E505, E677, K680, K724, R775, R778.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 15209 5 %RANDOM
Rwork0.216 ---
obs0.216 306185 89.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.6 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1-8.18 Å20 Å24.81 Å2
2---7.98 Å20 Å2
3----0.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25326 0 174 1154 26654
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.012
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.472.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 2109 4.9 %
Rwork0.293 40942 -
obs--75.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM_NEW.PLPTOP_NEW.PLP
X-RAY DIFFRACTION4PO4_XPLOR_PAR.TXTPO4_XPLOR_TOP.TXT
X-RAY DIFFRACTION5FORMIC_ACID.PARAMFORMIC_ACID.TOP
X-RAY DIFFRACTION6EGLY_XPLOR_PAR.TXTEGLY_XPLOR_TOP.TXT

+
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