[English] 日本語
Yorodumi
- PDB-2y4l: MANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH Manganese and GDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y4l
TitleMANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH Manganese and GDP
ComponentsMANNOSYLGLYCERATE SYNTHASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


mannosylglycerate synthase / mannosylglycerate synthase activity / mannosylglycerate biosynthetic process / hexosyltransferase activity / identical protein binding / metal ion binding
Similarity search - Function
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
GUANOSINE-5'-DIPHOSPHATE / MALONATE ION / : / Mannosylglycerate synthase / Mannosylglycerate synthase
Similarity search - Component
Biological speciesRHODOTHERMUS MARINUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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: 2XW4
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_asym_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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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)90,96017
Polymers89,2012
Non-polymers1,75915
Water1,820101
1
A: MANNOSYLGLYCERATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3877
Polymers44,6011
Non-polymers7866
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MANNOSYLGLYCERATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,57310
Polymers44,6011
Non-polymers9739
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.756, 149.756, 154.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 44600.688 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-382 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL TRUNCATION OF LAST 15 RESIDUES / Source: (gene. exp.) RHODOTHERMUS MARINUS (bacteria) / Strain: DSM 4252 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): TUNER
References: UniProt: Q9RFR0, UniProt: D0MI02*PLUS, mannosyl-3-phosphoglycerate synthase

-
Non-polymers , 5 types, 116 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLN 201 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 202 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLN 201 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 202 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLN 201 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLN 202 TO ALA
Nonpolymer detailsETHYLENE GLYCOL (EDO): ETHYLENE GLYCOL WAS THE CRYSTAL CRYOPROTECTANT. MALONATE (MLI): 0.4 M NA ...ETHYLENE GLYCOL (EDO): ETHYLENE GLYCOL WAS THE CRYSTAL CRYOPROTECTANT. MALONATE (MLI): 0.4 M NA MALONATE WAS THE PRECIPITATING AGENT USED DURING CRYSTALLIZATION. GUANOSINE-5'-DIPHOSPHATE (GDP): GDP IS THE NUCLEOTIDE PRODUCT FOLLOWING MGS CATALYZED MANNOSYL TRANSFER. MANGANESE (MN): 0.2 M MNCL2 WAS PRESENT IN THE MOTHER LIQUOR DURING CRYSTALLIZATION.
Sequence detailsC-TERMINAL TRUNCATION OF LAST 15 RESIDUES. Q201 AND Q202 WERE BOTH MUTATED TO ALANINES FOR SURFACE ...C-TERMINAL TRUNCATION OF LAST 15 RESIDUES. Q201 AND Q202 WERE BOTH MUTATED TO ALANINES FOR SURFACE ENTROPY MINIMIZATION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.61 Å3/Da / Density % sol: 78.1 % / Description: NONE
Crystal growpH: 5
Details: 4% V/V ETHYLENE GLYCOL, 0.1 M BIS-TRIS PROPANE PH 5.5, 0.2 MNCL2, 0.4 M SODIUM MALONATE.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9789
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 47314 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.9 % / Biso Wilson estimate: 54.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BO7

2bo7


Resolution: 2.8→129.69 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.501 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22041 2530 5.1 %RANDOM
Rwork0.18762 ---
obs0.1893 47314 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.073 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.25 Å20 Å2
2---0.49 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.8→129.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6179 0 108 101 6388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216488
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.671.9498831
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2075762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2822.067329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.61151006
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6121568
X-RAY DIFFRACTIONr_chiral_restr0.1120.2937
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215044
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_it0.8371.53786
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67626108
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.47132702
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2134.52719
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
LS refinement shellResolution: 2.797→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 179 -
Rwork0.3 3400 -
obs--98.3 %

+
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