[English] 日本語
Yorodumi
- PDB-4udg: Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4udg
TitleCrystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.60 Angstrom in complex with N-acetylglucosamine and inorganic phosphate
ComponentsUHGB_MP
KeywordsTRANSFERASE / GLYCOSIDE HYDROLASE FAMILY 130 / B-1 / 4-MANNOPYRANOSYL-CHITOBIOSE PHOSPHORYLASE / N-GLYCAN PHOSPHOROLYSIS
Function / homology
Function and homology information


glycosyltransferase activity
Similarity search - Function
Mannoside phosphorylase / beta-1,4-mannooligosaccharide phosphorylase / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
: / 2-acetamido-2-deoxy-alpha-D-glucopyranose / PHOSPHATE ION / Glycosidase
Similarity search - Component
Biological speciesUNCULTURED ORGANISM (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLadeveze, S. / Cioci, G. / Potocki-Veronese, G. / Tranier, S. / Mourey, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural Bases for N-Glycan Processing by Mannoside Phosphorylase.
Authors: Ladeveze, S. / Cioci, G. / Roblin, P. / Mourey, L. / Tranier, S. / Potocki-Veronese, G.
History
DepositionDec 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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: UHGB_MP
B: UHGB_MP
C: UHGB_MP
D: UHGB_MP
E: UHGB_MP
F: UHGB_MP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,01536
Polymers235,9296
Non-polymers3,08730
Water26,3561463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27460 Å2
ΔGint-97.7 kcal/mol
Surface area60290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.816, 140.912, 168.598
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Sugars , 2 types, 12 molecules ABCDEF

#1: Protein
UHGB_MP


Mass: 39321.422 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) UNCULTURED ORGANISM (environmental samples)
Description: FECAL SAMPLE FROM HOMO SAPIENS / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI
References: UniProt: D9ZDQ9, Transferases; Glycosyltransferases; Hexosyltransferases
#3: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 5 types, 1487 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1463 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.74 % / Description: NONE
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 17.5% PEG 3350, 200 MM NH4CL, PH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2014 / Details: PAIR OF KB MIRRORS FOR ADJUSTABLE FOCUSING
RadiationMonochromator: CHANNEL-CUT DOUBLE CRYSTAL MONOCHROMATOR (CINEL), CRYOCOOLED, 6MM GAP
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.6→47 Å / Num. obs: 261651 / % possible obs: 99.9 % / Observed criterion σ(I): -1 / Redundancy: 9.37 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.49
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2.07 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VKD

1vkd


Resolution: 1.6→108.12 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.955 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.18297 13154 5 %RANDOM
Rwork0.15361 ---
obs0.15507 248496 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.301 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.56 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.6→108.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15410 0 188 1463 17061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01916498
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214840
X-RAY DIFFRACTIONr_angle_refined_deg1.891.94522549
X-RAY DIFFRACTIONr_angle_other_deg0.919334213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96852001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.88322.868802
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.736152398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.25215118
X-RAY DIFFRACTIONr_chiral_restr0.1290.22321
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02118910
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024134
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5191.537878
X-RAY DIFFRACTIONr_mcbond_other1.5181.537877
X-RAY DIFFRACTIONr_mcangle_it2.2122.2899903
X-RAY DIFFRACTIONr_mcangle_other2.2122.2899904
X-RAY DIFFRACTIONr_scbond_it2.4791.8018620
X-RAY DIFFRACTIONr_scbond_other2.4791.8018620
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.712.60112641
X-RAY DIFFRACTIONr_long_range_B_refined5.3513.61419578
X-RAY DIFFRACTIONr_long_range_B_other5.34713.60319562
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 956 -
Rwork0.264 17978 -
obs--98.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.13110.0278-0.02880.3428-0.03210.07480.00420.01910.0011-0.0154-0.00850.0595-0.01050.02070.00430.04920.006-0.01050.019-0.00070.0617.150417.47272.0974
20.2690.0114-0.02440.18190.04830.095-0.00310.0262-0.00060.0082-0.01190.03330.03460.01150.01510.0729-0.0004-0.00130.0107-0.01220.058426.4216-23.32251.9067
30.238-0.05030.00730.2994-0.00560.08210.00520.019-0.0013-0.022-0.0127-0.02480.00490.00280.00750.0459-0.00090.00440.02720.00860.050756.95665.16851.6448
40.1181-0.10250.01720.1516-0.01340.1911-0.033-0.0131-0.02750.06470.00250.04080.03050.01280.03050.12450.00520.05030.01270.01490.037422.1348-21.211840.4296
50.19460.07120.02520.0645-0.04640.20910.0044-0.02460.00220.0484-0.0030.0212-0.04620.0006-0.00140.1174-0.00290.03710.0214-0.01080.027921.480120.48340.5906
60.24540.0433-0.15320.2643-0.02940.1024-0.003-0.1001-0.02650.0644-0.0267-0.013-0.01080.07340.02980.0959-0.0012-0.02440.0690.02650.018157.92120.195339.9764
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 702
2X-RAY DIFFRACTION2B7 - 680
3X-RAY DIFFRACTION3C8 - 665
4X-RAY DIFFRACTION4D8 - 681
5X-RAY DIFFRACTION5E7 - 679
6X-RAY DIFFRACTION6F8 - 646

+
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