[English] 日本語
Yorodumi
- PDB-3kia: Crystal structure of mannosyl-3-phosphoglycerate synthase from Ru... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kia
TitleCrystal structure of mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus
ComponentsMannosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE / GT-A TYPE GLYCOSYLTRANSFERASE / GT-81 / MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE / RUBROBACTER XYLANOPHILUS / GDP-MANNOSE / Glycosyltransferase
Function / homology
Function and homology information


mannosyl-3-phosphoglycerate synthase activity / glucosyl-3-phosphoglycerate synthase / metal ion binding
Similarity search - Function
: / Glycosyltransferase 2-like / Glycosyl transferase family 2 / 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'-MONOPHOSPHATE / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciessynthetic construct (others)
Rubrobacter xylanophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMacedo-Ribeiro, S. / Pereira, P.J.B. / Empadinhas, N. / da Costa, M.S.
CitationJournal: Mol.Microbiol. / Year: 2011
Title: Functional and structural characterization of a novel mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus reveals its dual substrate specificity
Authors: Empadinhas, N. / Pereira, P.J.B. / Albuquerque, L. / Costa, J. / Sa-Moura, B. / Marques, A.T. / Macedo-Ribeiro, S. / da Costa, M.S.
History
DepositionNov 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_asym_id / _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_asym_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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: Mannosyl-3-phosphoglycerate synthase
C: Mannosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,00110
Polymers86,0952
Non-polymers9068
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-43 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.010, 109.010, 313.418
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Mannosyl-3-phosphoglycerate synthase


Mass: 43047.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Rubrobacter xylanophilus (bacteria)
Strain: DSM 9941 / Gene: 266117 / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: B7SY86, mannosyl-3-phosphoglycerate synthase
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE N-TERMINAL SEQUENCE MHHHHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTDDDDKAMADIGSEF CORRESPONDS TO THE ...THE N-TERMINAL SEQUENCE MHHHHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTDDDDKAMADIGSEF CORRESPONDS TO THE EXPRESSION TAG AND LINKER.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 0.1M MES pH 6.0, 2.0M NaCl, 0.1M NaH2PO4, 0.1M KH2PO4, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.8→90.5 Å / Num. all: 27781 / Num. obs: 27781 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 53.51 Å2 / Rsym value: 0.061 / Net I/σ(I): 10.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.31

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3f1y

3f1y


Resolution: 2.8→53.699 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.32 / σ(F): 0 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 1380 5.01 %
Rwork0.1899 26151 -
obs0.1924 27531 97.93 %
all-27348 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.995 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 145.22 Å2 / Biso mean: 53.9491 Å2 / Biso min: 21.77 Å2
Baniso -1Baniso -2Baniso -3
1-6.403 Å2-0 Å2-0 Å2
2--6.403 Å20 Å2
3----12.8061 Å2
Refinement stepCycle: LAST / Resolution: 2.8→53.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4855 0 54 106 5015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095018
X-RAY DIFFRACTIONf_angle_d0.9146812
X-RAY DIFFRACTIONf_dihedral_angle_d16.8531907
X-RAY DIFFRACTIONf_chiral_restr0.319744
X-RAY DIFFRACTIONf_plane_restr0.004898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90010.39171100.30082500X-RAY DIFFRACTION96
2.9001-3.01620.32591420.2332507X-RAY DIFFRACTION97
3.0162-3.15340.25341170.22482557X-RAY DIFFRACTION97
3.1534-3.31970.26031530.20322539X-RAY DIFFRACTION98
3.3197-3.52760.26551400.20562589X-RAY DIFFRACTION98
3.5276-3.79990.21161190.18472621X-RAY DIFFRACTION99
3.7999-4.18220.22831360.16822642X-RAY DIFFRACTION99
4.1822-4.7870.21231430.15082645X-RAY DIFFRACTION99
4.787-6.02990.21991570.17892708X-RAY DIFFRACTION99
6.0299-53.70890.22421630.1942843X-RAY DIFFRACTION98
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)
12.0568-0.25410.53342.8846-0.08670.29960.0295-0.11090.00940.0728-0.1356-0.1859-0.27930.21590.12010.2282-0.1934-0.03230.3770.1510.202955.379-19.2559-2.7283
21.00890.33540.15851.6910.16330.1590.1602-0.0464-0.11380.4702-0.3812-0.0696-0.20820.21280.18770.3761-0.1269-0.05240.50690.12980.269949.5585-30.28394.7665
31.15191.1908-0.53591.253-0.02310.8375-0.02540.37810.1744-0.15390.0263-0.17390.01460.0528-0.0080.2281-0.01480.03850.39910.15040.291333.3445-38.7192-3.362
43.01032.177-0.54813.49440.64731.07810.74830.3431.16790.0245-0.66130.42270.2754-0.4752-0.31610.2098-0.00420.09790.36380.12590.366957.1086-38.5692-12.2387
50.85050.2547-0.22151.6822-0.54521.14010.08830.12620.12740.0426-0.01530.3048-0.1978-0.1872-0.10790.2120.07530.05940.39710.10140.35529.7941-36.597614.3093
61.50570.8759-0.5760.349-0.2740.72890.2003-0.0494-0.16240.1012-0.14520.0595-0.1088-0.0222-0.03830.24180.01290.03570.4310.13930.300424.1492-40.84729.8886
70.92580.29590.09580.38020.39081.40730.293-0.2180.2702-0.2474-0.28760.2877-0.4931-0.0967-0.06990.6372-0.1620.01250.53370.09990.395543.075-32.342319.6277
80.1053-0.34460.07721.79130.0233.32920.02980.0552-0.19840.1419-0.0104-0.31720.30130.80740.16860.2778-0.04630.04380.5470.21780.42420.96-51.348524.1714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 14:179)
2X-RAY DIFFRACTION2(chain A and resid 180:255)
3X-RAY DIFFRACTION3(chain A and resid 256:322)
4X-RAY DIFFRACTION4(chain A and resid 323:333)
5X-RAY DIFFRACTION5(chain C and resid 9:186)
6X-RAY DIFFRACTION6(chain C and resid 187:285)
7X-RAY DIFFRACTION7(chain C and resid 286:321)
8X-RAY DIFFRACTION8(chain C and resid 322:333)

+
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