[English] 日本語
Yorodumi
- PDB-2bo7: DISSECTION OF MANNOSYLGLYCERATE SYNTHASE: AN ARCHETYPAL MANNOSYLT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bo7
TitleDISSECTION OF MANNOSYLGLYCERATE SYNTHASE: AN ARCHETYPAL MANNOSYLTRANSFERASE
ComponentsMANNOSYLGLYCERATE SYNTHASE
KeywordsTRANSFERASE / CATALYSIS / GLYCOSYLTRANSFERASE / MANNOSE / STEREOSELECTIVITY
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 / Mannosylglycerate synthase
Similarity search - Component
Biological speciesRHODOTHERMUS MARINUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsFlint, J. / Taylor, E. / Yang, M. / Bolam, D.N. / Tailford, L.E. / Martinez-Fleites, C. / Dodson, E.J. / Davis, B.G. / Gilbert, H.J. / Davies, G.J.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2005
Title: Structural dissection and high-throughput screening of mannosylglycerate synthase.
Authors: Flint, J. / Taylor, E. / Yang, M. / Bolam, D.N. / Tailford, L.E. / Martinez-Fleites, C. / Dodson, E.J. / Davis, B.G. / Gilbert, H.J. / Davies, G.J.
History
DepositionApr 8, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_assembly / pdbx_struct_assembly_prop
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_struct_assembly.method_details
Revision 1.3Dec 13, 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MANNOSYLGLYCERATE SYNTHASE
B: MANNOSYLGLYCERATE SYNTHASE
C: MANNOSYLGLYCERATE SYNTHASE
D: MANNOSYLGLYCERATE SYNTHASE
E: MANNOSYLGLYCERATE SYNTHASE
F: MANNOSYLGLYCERATE SYNTHASE
G: MANNOSYLGLYCERATE SYNTHASE
H: MANNOSYLGLYCERATE SYNTHASE
I: MANNOSYLGLYCERATE SYNTHASE
J: MANNOSYLGLYCERATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,88630
Polymers461,86510
Non-polymers5,02120
Water2,288127
1
A: MANNOSYLGLYCERATE SYNTHASE
B: MANNOSYLGLYCERATE SYNTHASE
C: MANNOSYLGLYCERATE SYNTHASE
D: MANNOSYLGLYCERATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,75412
Polymers184,7464
Non-polymers2,0098
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12630 Å2
ΔGint-128 kcal/mol
Surface area53720 Å2
MethodPISA
2
E: MANNOSYLGLYCERATE SYNTHASE
F: MANNOSYLGLYCERATE SYNTHASE
G: MANNOSYLGLYCERATE SYNTHASE
H: MANNOSYLGLYCERATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,75412
Polymers184,7464
Non-polymers2,0098
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12730 Å2
ΔGint-128 kcal/mol
Surface area53650 Å2
MethodPISA
3
I: MANNOSYLGLYCERATE SYNTHASE
J: MANNOSYLGLYCERATE SYNTHASE
hetero molecules

I: MANNOSYLGLYCERATE SYNTHASE
J: MANNOSYLGLYCERATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,75412
Polymers184,7464
Non-polymers2,0098
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area12770 Å2
ΔGint-131 kcal/mol
Surface area53700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)406.699, 162.140, 108.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A2 - 500
2111B2 - 500
3111C2 - 500
4111D2 - 500
5111E2 - 500
6111F2 - 500
7111G2 - 500
8111H2 - 500
9111I2 - 500
10111J2 - 500

-
Components

#1: Protein
MANNOSYLGLYCERATE SYNTHASE /


Mass: 46186.473 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOTHERMUS MARINUS (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER
References: UniProt: Q9RFR0, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.5 Å3/Da / Density % sol: 72.2 %
Crystal growDetails: 10 MM NACL, 0.1 M SODIUM ACETATE TRIHYDRATE, PH 4.6, 15% (V/V) MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.95→40 Å / Num. obs: 151344 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.4 / % possible all: 93

-
Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKLdata reduction
HKLdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BO6

2bo6


Resolution: 2.95→223.61 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.919 / SU B: 29.694 / SU ML: 0.255 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.915 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 7443 5 %RANDOM
Rwork0.207 ---
obs0.208 140625 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2--0.71 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.95→223.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31020 0 290 127 31437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02132210
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.93243880
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.29753730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29922.1431680
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.176155140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.07715350
X-RAY DIFFRACTIONr_chiral_restr0.1080.24650
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0225080
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.214455
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.222007
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2933
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4680.2190
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4370.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2891.518987
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.39230280
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.76315115
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0424.513600
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

Ens-ID: 1 / Number: 3131 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.070.05
2Btight positional0.070.05
3Ctight positional0.060.05
4Dtight positional0.060.05
5Etight positional0.060.05
6Ftight positional0.030.05
7Gtight positional0.040.05
8Htight positional0.030.05
9Itight positional0.040.05
10Jtight positional0.040.05
1Atight thermal0.130.5
2Btight thermal0.130.5
3Ctight thermal0.080.5
4Dtight thermal0.090.5
5Etight thermal0.10.5
6Ftight thermal0.070.5
7Gtight thermal0.070.5
8Htight thermal0.060.5
9Itight thermal0.060.5
10Jtight thermal0.070.5
LS refinement shellResolution: 2.95→3.03 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.359 443
Rwork0.324 9237
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)
12.10580.4578-0.01832.2083-0.59641.5674-0.0142-0.08720.0318-0.0050.01520.1730.2593-0.1073-0.0011-0.22390.05780.0388-0.4613-0.0194-0.435794.18230.29816.584
21.4347-0.39440.81592.9062-1.03882.8447-0.05580.1838-0.1168-0.15190.0445-0.0188-0.13950.08630.0113-0.3458-0.02850.0407-0.4716-0.0208-0.418893.43474.65-1.405
32.157-0.26830.08582.3911.52.98050.2140.1460.0895-0.0558-0.15850.1536-0.035-0.5154-0.0556-0.40550.11150.0887-0.08120.0086-0.138555.19764.8845.567
42.8643-0.3741-1.09751.2846-0.03282.32150.0640.3557-0.193-0.2001-0.15980.23180.5321-0.3390.0958-0.082-0.0467-0.0473-0.0643-0.1543-0.273373.68827.572-18.02
51.7298-0.0320.12572.5560.4452.3146-0.0554-0.20490.02410.0071-0.0775-0.1685-0.18180.04170.1329-0.09170.14120.0156-0.14590.0495-0.4466111.73131.47749.256
65.55540.73850.69421.7572-0.2822.1991-0.0352-0.3211.48340.0723-0.1927-0.3142-0.98520.2640.22780.8558-0.1453-0.09610.06250.06720.4308137.38471.9150.687
75.6143-0.98180.14081.5458-0.2581.91610.0324-0.89780.1010.082-0.1794-0.2365-0.2101-0.12350.147-0.0416-0.04550.0190.39780.0607-0.356129.1632.2685.339
82.345-0.2956-0.34621.2561-0.38443.42270.09880.14130.2458-0.1417-0.1049-0.1215-0.39750.34370.00610.0897-0.210.04240.44590.29330.0846164.05842.00354.178
92.4548-0.0409-0.27772.0983-0.80012.30640.21980.39910.0898-0.2482-0.1264-0.0798-0.06880.4112-0.0934-0.2058-0.14140.03510.69190.15140.0206189.42514.49256.168
103.7565-1.440.39032.3737-0.68841.8193-0.0113-0.2201-0.43960.14210.130.13520.21610.4229-0.1187-0.3565-0.16040.06760.32140.11060.1559184.943-7.89298.418
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 382
2X-RAY DIFFRACTION2B2 - 382
3X-RAY DIFFRACTION3C2 - 382
4X-RAY DIFFRACTION4D2 - 382
5X-RAY DIFFRACTION5E2 - 382
6X-RAY DIFFRACTION6F2 - 382
7X-RAY DIFFRACTION7G2 - 382
8X-RAY DIFFRACTION8H2 - 382
9X-RAY DIFFRACTION9I2 - 382
10X-RAY DIFFRACTION10J2 - 382

+
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