[English] 日本語
Yorodumi
- PDB-6gh3: Paenibacillus sp. YM1 laminaribiose phosphorylase with alpha-man-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gh3
TitlePaenibacillus sp. YM1 laminaribiose phosphorylase with alpha-man-1-phosphate bound
ComponentsLaminaribiose phosphorylase
KeywordsHYDROLASE / laminaribiose phosphorylase / Glycosyl hydrolase 94 / disaccharide synthesis / CARBOHYDRATE
Function / homology
Function and homology information


laminaribiose phosphorylase / laminaribiose phosphorylase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 36 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
1-O-phosphono-alpha-D-mannopyranose / Laminaribiose phosphorylase
Similarity search - Component
Biological speciesPaenibacillus sp. YM1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.82 Å
AuthorsKuhaudomlarp, S. / Walpole, S. / Stevenson, C.E.M. / Nepogodiev, S.A. / Lawson, D.M. / Angulo, J. / Field, R.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P010660/1 United Kingdom
Engineering and Physical Sciences Research CouncilBB/M02903411 United Kingdom
CitationJournal: Chembiochem / Year: 2019
Title: Unravelling the Specificity of Laminaribiose Phosphorylase from Paenibacillus sp. YM-1 towards Donor Substrates Glucose/Mannose 1-Phosphate by Using X-ray Crystallography and Saturation ...Title: Unravelling the Specificity of Laminaribiose Phosphorylase from Paenibacillus sp. YM-1 towards Donor Substrates Glucose/Mannose 1-Phosphate by Using X-ray Crystallography and Saturation Transfer Difference NMR Spectroscopy.
Authors: Kuhaudomlarp, S. / Walpole, S. / Stevenson, C.E.M. / Nepogodiev, S.A. / Lawson, D.M. / Angulo, J. / Field, R.A.
History
DepositionMay 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Laminaribiose phosphorylase
B: Laminaribiose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,27221
Polymers203,7352
Non-polymers1,53719
Water12,520695
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, PISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-35 kcal/mol
Surface area57940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.570, 146.570, 222.227
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 4 - 908 / Label seq-ID: 6 - 910

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Laminaribiose phosphorylase /


Mass: 101867.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Two residues with sequence Gly-Pro are appended to the N-terminus which are left over after cleavage of the tag
Source: (gene. exp.) Paenibacillus sp. YM1 (bacteria) / Gene: lbpA / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D7UT17, laminaribiose phosphorylase
#3: Sugar ChemComp-M1P / 1-O-phosphono-alpha-D-mannopyranose / ALPHA-D-MANNOSE 1-PHOSPHATE / 1-O-phosphono-alpha-D-mannose / 1-O-phosphono-D-mannose / 1-O-phosphono-mannose / Mannose 1-phosphate


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Manp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 4 types, 712 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Null

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.82→73.29 Å / Num. obs: 215182 / % possible obs: 100 % / Redundancy: 9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.041 / Rrim(I) all: 0.126 / Net I/σ(I): 12.7 / Num. measured all: 1928822 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.82-1.859.21.992105800.4070.682.108100
9.97-73.297.60.03115250.9990.0110.03399.6

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.31data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6GGY

6ggy


Resolution: 1.82→73.29 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.316 / SU ML: 0.106 / SU R Cruickshank DPI: 0.1152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.109
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 10878 5.1 %RANDOM
Rwork0.194 ---
obs0.1952 204179 99.92 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.1 Å2 / Biso mean: 39.822 Å2 / Biso min: 12.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--0.5 Å20 Å2
3----0.99 Å2
Refinement stepCycle: final / Resolution: 1.82→73.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13931 0 94 720 14745
Biso mean--42.36 34.39 -
Num. residues----1801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01914483
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212984
X-RAY DIFFRACTIONr_angle_refined_deg1.41.94719659
X-RAY DIFFRACTIONr_angle_other_deg0.957329907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12551826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9923.319696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.523152226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.38215116
X-RAY DIFFRACTIONr_chiral_restr0.0830.22100
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216585
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023228
Refine LS restraints NCS

Ens-ID: 1 / Number: 59302 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.82→1.867 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 774 -
Rwork0.354 14972 -
all-15746 -
obs--99.81 %
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)
10.808-0.1386-0.37970.61680.30162.0049-0.23910.1556-0.18450.1466-0.06420.04730.7209-0.32520.30330.4306-0.19920.18980.1313-0.09060.094351.6251-1.478456.1618
22.0274-0.64460.53491.47530.53192.8685-0.08010.1954-0.01850.1949-0.4380.40810.4939-1.13160.51810.2754-0.35580.18890.7242-0.31180.204235.50014.214435.6959
34.25172.2207-0.51047.00420.27383.62120.1323-0.3827-0.24030.7943-0.2919-0.07050.0134-0.47690.15970.1097-0.03110.03440.7818-0.28720.268124.576420.946737.0917
42.08-0.0612-1.17374.62541.63822.82720.1859-0.07080.29260.3625-0.49260.4095-0.2356-0.82050.30670.18440.00460.03950.9715-0.3650.311917.250427.158738.8107
53.17710.36550.08511.04720.11391.51870.0929-0.01110.2055-0.0415-0.38830.4863-0.163-0.81930.29540.12450.1229-0.03120.9374-0.43820.331921.249828.774223.3246
60.6798-0.28680.2631.18680.15861.70480.05760.15030.0345-0.0928-0.43010.1947-0.0489-0.59980.37240.06060.0030.00690.5325-0.23170.125239.223319.366520.0258
71.5693-0.0910.1733.3541.6883.11940.00520.0768-0.165-0.0749-0.25080.6320.563-0.83980.24570.3723-0.40470.11920.9655-0.41870.345825.2083-6.231916.9398
86.01892.7221.028310.6032.65954.10310.0224-0.068-0.43070.45430.0894-0.80020.47190.3461-0.11180.13120.06010.01370.20910.02310.094480.82119.051669.456
90.91480.0723-0.14550.57660.21151.5683-0.06160.0768-0.03650.02840.0029-0.03670.12450.12810.05870.077-0.02220.02870.0981-0.0040.015273.513820.898946.7023
101.56340.95650.77682.61411.23514.5365-0.019-0.0350.26770.05530.009-0.0223-0.1460.31420.01010.1054-0.01510.01620.0732-0.01540.069371.259433.71468.5599
114.64350.4902-0.58282.2932-0.41522.24030.10240.51580.1795-0.16710.12720.117-0.2857-0.1667-0.22960.32140.05310.06220.08780.05690.082952.076249.449668.4781
121.3057-0.0654-0.59132.1476-0.80492.0160.18450.0720.2980.14890.05120.1489-0.5149-0.1942-0.23570.29560.04620.09740.0840.0150.089545.720546.479184.2041
131.08480.2129-0.8840.78810.3571.8126-0.0617-0.0873-0.01320.08230.04190.02380.03760.1090.01990.1406-0.00340.01560.04950.010.004160.84826.673279.6384
142.8565-0.32890.71442.6024-1.10212.649-0.0213-0.35660.52490.46670.0655-0.3021-0.72590.7549-0.04410.4239-0.1981-0.01470.4762-0.12640.203380.111847.519487.0368
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 323
2X-RAY DIFFRACTION2A324 - 387
3X-RAY DIFFRACTION3A388 - 442
4X-RAY DIFFRACTION4A443 - 492
5X-RAY DIFFRACTION5A493 - 598
6X-RAY DIFFRACTION6A599 - 799
7X-RAY DIFFRACTION7A800 - 911
8X-RAY DIFFRACTION8B4 - 23
9X-RAY DIFFRACTION9B24 - 323
10X-RAY DIFFRACTION10B324 - 370
11X-RAY DIFFRACTION11B371 - 480
12X-RAY DIFFRACTION12B481 - 704
13X-RAY DIFFRACTION13B705 - 805
14X-RAY DIFFRACTION14B806 - 908

+
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