[English] 日本語
Yorodumi
- PDB-2y4j: MANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH LACTATE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y4j
TitleMANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH LACTATE
ComponentsMANNOSYLGLYCERATE SYNTHASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / GT FAMILY 78 MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE
Function / homology
Function and homology information


mannosylglycerate synthase / mannosylglycerate synthase activity / mannosylglycerate biosynthetic process / hexosyltransferase activity / metal ion binding / identical protein binding
Similarity search - Function
: / : / Mannosylglycerate synthase C-terminal domain / Mannosylglycerate synthase, GT domain / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
LACTIC ACID / Mannosylglycerate synthase
Similarity search - Component
Biological speciesRHODOTHERMUS MARINUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNielsen, M.M. / Suits, M.D.L. / Yang, M. / Barry, C.S. / Martinez-Fleites, C. / Tailford, L.E. / Flint, J.E. / Davis, B.G. / Davies, G.J. / Gilbert, H.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Substrate and Metal Ion Promiscuity in Mannosylglycerate Synthase.
Authors: Nielsen, M.M. / Suits, M.D.L. / Yang, M. / Barry, C.S. / Martinez-Fleites, C. / Tailford, L.E. / Flint, J.E. / Dumon, C. / Davis, B.G. / Gilbert, H.J. / Davies, G.J.
History
DepositionJan 7, 2011Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 2, 2011ID: 2XW2
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references / Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_atom_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 / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MANNOSYLGLYCERATE SYNTHASE
B: MANNOSYLGLYCERATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9008
Polymers89,4302
Non-polymers4706
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-25 kcal/mol
Surface area28610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.975, 148.975, 154.973
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22A
13B
23A

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPROBB2 - 1082 - 108
21SERSERPROPROAA2 - 1082 - 108
12ASPASPILEILEBB109 - 263109 - 263
22ASPASPILEILEAA109 - 263109 - 263
13ALAALAGLUGLUBB264 - 381264 - 381
23ALAALAGLUGLUAA264 - 381264 - 381

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein MANNOSYLGLYCERATE SYNTHASE / MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE


Mass: 44714.789 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-382
Source method: isolated from a genetically manipulated source
Details: TRUNCATION / Source: (gene. exp.) RHODOTHERMUS MARINUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): TUNER
References: UniProt: Q9RFR0, mannosyl-3-phosphoglycerate synthase
#2: Chemical ChemComp-LAC / LACTIC ACID


Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsLACTATE (LAC): LACTATE IS A MANNOSE ACCEPTOR
Sequence detailsC-TERMINAL TRUNCATION

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5 Å3/Da / Density % sol: 75.3 % / Description: NONE
Crystal growpH: 5
Details: 0.3 M SODIUM D-LACTATE, 0.1 M SODIUM ACETATE TRIHYDRATE, PH 4.6, 40% (V/V) 2-METHYL-1, 3-PROPANEDIOL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 2.3→67 Å / Num. obs: 83970 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.4 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BO7

2bo7


Resolution: 2.3→129.02 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.317 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22163 4435 5 %RANDOM
Rwork0.19816 ---
obs0.19934 83970 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.807 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→129.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6125 0 30 295 6450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216337
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9398632
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6845754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43522.375320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.68315987
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3531561
X-RAY DIFFRACTIONr_chiral_restr0.1080.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214935
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8571.53772
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68726081
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.64532565
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4274.52549
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
12A428medium positional0.190.5
11B428medium positional0.190.5
22A599medium positional0.130.5
21B599medium positional0.130.5
32A471medium positional0.090.5
31B471medium positional0.090.5
12A406loose positional0.345
11B406loose positional0.345
22A613loose positional0.265
21B613loose positional0.265
32A501loose positional0.295
31B501loose positional0.295
12A428medium thermal1.232
11B428medium thermal1.232
22A599medium thermal1.052
21B599medium thermal1.052
32A471medium thermal0.692
31B471medium thermal0.692
12A406loose thermal1.2510
11B406loose thermal1.2510
22A613loose thermal1.1510
21B613loose thermal1.1510
32A501loose thermal0.9910
31B501loose thermal0.9910
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 324 -
Rwork0.287 6157 -
obs--99.98 %

+
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