[English] 日本語
Yorodumi
- PDB-3wiq: Crystal structure of kojibiose phosphorylase complexed with kojibiose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wiq
TitleCrystal structure of kojibiose phosphorylase complexed with kojibiose
ComponentsKojibiose phosphorylase
KeywordsTRANSFERASE / (alpha/alpha)6 barrel / Phosphorylase
Function / homology
Function and homology information


kojibiose phosphorylase / kojibiose phosphorylase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Maltose phosphorylase/glycosyl hydrolase/vacuolar acid trehalase / Glycoside hydrolase, family 65, central catalytic / Glycoside hydrolase, family 65, N-terminal / Glycosyl hydrolase family 65 central catalytic domain / Glycosyl hydrolase family 65, N-terminal domain / Glycoside hydrolase family 65, C-terminal / Glycosyl hydrolase family 65, C-terminal domain / Glycoside hydrolase, family 65, N-terminal domain / Maltose phosphorylase, domain 3 / Maltose phosphorylase, domain 3 ...Maltose phosphorylase/glycosyl hydrolase/vacuolar acid trehalase / Glycoside hydrolase, family 65, central catalytic / Glycoside hydrolase, family 65, N-terminal / Glycosyl hydrolase family 65 central catalytic domain / Glycosyl hydrolase family 65, N-terminal domain / Glycoside hydrolase family 65, C-terminal / Glycosyl hydrolase family 65, C-terminal domain / Glycoside hydrolase, family 65, N-terminal domain / Maltose phosphorylase, domain 3 / Maltose phosphorylase, domain 3 / Glycoside hydrolase family 65, N-terminal domain superfamily / Glycosyltransferase - #10 / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Kojibiose phosphorylase
Similarity search - Component
Biological speciesCaldicellulosiruptor saccharolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsOkada, S. / Yamamoto, T. / Watanabe, H. / Nishimoto, T. / Chaen, H. / Fukuda, S. / Wakagi, T. / Fushinobu, S.
Citation
Journal: Febs J. / Year: 2014
Title: Structural and mutational analysis of substrate recognition in kojibiose phosphorylase
Authors: Okada, S. / Yamamoto, T. / Watanabe, H. / Nishimoto, T. / Chaen, H. / Fukuda, S. / Wakagi, T. / Fushinobu, S.
#1: Journal: Biosci.Biotechnol.Biochem. / Year: 2011
Title: Enzymatic properties of recombinant kojibiose phosphorylase from Caldicellulosiruptor saccharolyticus ATCC43494
Authors: Yamamoto, T. / Nishio-Kosaka, M. / Izawa, S. / Aga, H. / Nishimoto, T. / Chaen, H. / Fukuda, S.
History
DepositionSep 24, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kojibiose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1243
Polymers88,6861
Non-polymers4382
Water1,17165
1
A: Kojibiose phosphorylase
hetero molecules

A: Kojibiose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,2486
Polymers177,3722
Non-polymers8774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,-y-1,-z1
Unit cell
Length a, b, c (Å)192.506, 192.506, 202.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein Kojibiose phosphorylase


Mass: 88685.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor saccharolyticus (bacteria)
Strain: ATCC 43494 / DSM 8903 / Gene: Csac_0444 / Plasmid: pRSET0439-C-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3)-RIL / References: UniProt: A4XGP2, kojibiose phosphorylase
#2: Polysaccharide alpha-D-glucopyranose-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsALPHA-1,2-LINKED GLC AND BGC IS KOJIBIOSE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.28 Å3/Da / Density % sol: 76.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5mM kojibiose, 0.2M NaCl, 2.0M (NH4)2SO4, 0.1M Na-cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2011
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 47021 / Num. obs: 47003 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.7 % / Rsym value: 0.105 / Net I/σ(I): 30
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 13.9 % / Num. unique all: 2315 / Rsym value: 0.982 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H54

1h54


Resolution: 2.8→48.13 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.903 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.975 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2338 5 %RANDOM
Rwork0.2045 ---
obs0.2072 44087 98.61 %-
all-44708 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 164.61 Å2 / Biso mean: 56.1333 Å2 / Biso min: 25.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6148 0 28 65 6241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196317
X-RAY DIFFRACTIONr_bond_other_d0.0020.025989
X-RAY DIFFRACTIONr_angle_refined_deg1.9551.9588538
X-RAY DIFFRACTIONr_angle_other_deg0.918313809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4665750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61924.904314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.202151145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.371527
X-RAY DIFFRACTIONr_chiral_restr0.1110.2921
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027082
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021463
LS refinement shellResolution: 2.795→2.868 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 170 -
Rwork0.296 3220 -
all-3390 -
obs--98.6 %

+
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