[English] 日本語
Yorodumi
- PDB-1c2y: CRYSTAL STRUCTURES OF A PENTAMERIC FUNGAL AND AN ICOSAHEDRAL PLAN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c2y
TitleCRYSTAL STRUCTURES OF A PENTAMERIC FUNGAL AND AN ICOSAHEDRAL PLANT LUMAZINE SYNTHASE REVEALS THE STRUCTURAL BASIS FOR DIFFERENCES IN ASSEMBLY
ComponentsPROTEIN (LUMAZINE SYNTHASE)
KeywordsTRANSFERASE / RIBOFLAVIN BIOSYNTHESIS
Function / homology
Function and homology information


6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / riboflavin biosynthetic process / chloroplast
Similarity search - Function
6,7-dimethyl-8-ribityllumazine synthase, chloroplast / Lumazine/riboflavin synthase / Lumazine synthase / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily / 6,7-dimethyl-8-ribityllumazine synthase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LMZ / 6,7-dimethyl-8-ribityllumazine synthase, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsPersson, K. / Schneider, G. / Jordan, D.B. / Viitanen, P.V. / Sandalova, T.
CitationJournal: Protein Sci. / Year: 1999
Title: Crystal structure analysis of a pentameric fungal and an icosahedral plant lumazine synthase reveals the structural basis for differences in assembly.
Authors: Persson, K. / Schneider, G. / Jordan, D.B. / Viitanen, P.V. / Sandalova, T.
History
DepositionJul 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 16, 2013Group: Structure summary
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_ref_seq_dif ...database_2 / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (LUMAZINE SYNTHASE)
B: PROTEIN (LUMAZINE SYNTHASE)
C: PROTEIN (LUMAZINE SYNTHASE)
D: PROTEIN (LUMAZINE SYNTHASE)
E: PROTEIN (LUMAZINE SYNTHASE)
F: PROTEIN (LUMAZINE SYNTHASE)
G: PROTEIN (LUMAZINE SYNTHASE)
H: PROTEIN (LUMAZINE SYNTHASE)
I: PROTEIN (LUMAZINE SYNTHASE)
J: PROTEIN (LUMAZINE SYNTHASE)
K: PROTEIN (LUMAZINE SYNTHASE)
L: PROTEIN (LUMAZINE SYNTHASE)
M: PROTEIN (LUMAZINE SYNTHASE)
N: PROTEIN (LUMAZINE SYNTHASE)
O: PROTEIN (LUMAZINE SYNTHASE)
P: PROTEIN (LUMAZINE SYNTHASE)
Q: PROTEIN (LUMAZINE SYNTHASE)
R: PROTEIN (LUMAZINE SYNTHASE)
S: PROTEIN (LUMAZINE SYNTHASE)
T: PROTEIN (LUMAZINE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,86040
Polymers331,05620
Non-polymers5,80520
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (LUMAZINE SYNTHASE)
B: PROTEIN (LUMAZINE SYNTHASE)
C: PROTEIN (LUMAZINE SYNTHASE)
D: PROTEIN (LUMAZINE SYNTHASE)
E: PROTEIN (LUMAZINE SYNTHASE)
F: PROTEIN (LUMAZINE SYNTHASE)
G: PROTEIN (LUMAZINE SYNTHASE)
H: PROTEIN (LUMAZINE SYNTHASE)
I: PROTEIN (LUMAZINE SYNTHASE)
J: PROTEIN (LUMAZINE SYNTHASE)
K: PROTEIN (LUMAZINE SYNTHASE)
L: PROTEIN (LUMAZINE SYNTHASE)
M: PROTEIN (LUMAZINE SYNTHASE)
N: PROTEIN (LUMAZINE SYNTHASE)
O: PROTEIN (LUMAZINE SYNTHASE)
P: PROTEIN (LUMAZINE SYNTHASE)
Q: PROTEIN (LUMAZINE SYNTHASE)
R: PROTEIN (LUMAZINE SYNTHASE)
S: PROTEIN (LUMAZINE SYNTHASE)
T: PROTEIN (LUMAZINE SYNTHASE)
hetero molecules

A: PROTEIN (LUMAZINE SYNTHASE)
B: PROTEIN (LUMAZINE SYNTHASE)
C: PROTEIN (LUMAZINE SYNTHASE)
D: PROTEIN (LUMAZINE SYNTHASE)
E: PROTEIN (LUMAZINE SYNTHASE)
F: PROTEIN (LUMAZINE SYNTHASE)
G: PROTEIN (LUMAZINE SYNTHASE)
H: PROTEIN (LUMAZINE SYNTHASE)
I: PROTEIN (LUMAZINE SYNTHASE)
J: PROTEIN (LUMAZINE SYNTHASE)
K: PROTEIN (LUMAZINE SYNTHASE)
L: PROTEIN (LUMAZINE SYNTHASE)
M: PROTEIN (LUMAZINE SYNTHASE)
N: PROTEIN (LUMAZINE SYNTHASE)
O: PROTEIN (LUMAZINE SYNTHASE)
P: PROTEIN (LUMAZINE SYNTHASE)
Q: PROTEIN (LUMAZINE SYNTHASE)
R: PROTEIN (LUMAZINE SYNTHASE)
S: PROTEIN (LUMAZINE SYNTHASE)
T: PROTEIN (LUMAZINE SYNTHASE)
hetero molecules

A: PROTEIN (LUMAZINE SYNTHASE)
B: PROTEIN (LUMAZINE SYNTHASE)
C: PROTEIN (LUMAZINE SYNTHASE)
D: PROTEIN (LUMAZINE SYNTHASE)
E: PROTEIN (LUMAZINE SYNTHASE)
F: PROTEIN (LUMAZINE SYNTHASE)
G: PROTEIN (LUMAZINE SYNTHASE)
H: PROTEIN (LUMAZINE SYNTHASE)
I: PROTEIN (LUMAZINE SYNTHASE)
J: PROTEIN (LUMAZINE SYNTHASE)
K: PROTEIN (LUMAZINE SYNTHASE)
L: PROTEIN (LUMAZINE SYNTHASE)
M: PROTEIN (LUMAZINE SYNTHASE)
N: PROTEIN (LUMAZINE SYNTHASE)
O: PROTEIN (LUMAZINE SYNTHASE)
P: PROTEIN (LUMAZINE SYNTHASE)
Q: PROTEIN (LUMAZINE SYNTHASE)
R: PROTEIN (LUMAZINE SYNTHASE)
S: PROTEIN (LUMAZINE SYNTHASE)
T: PROTEIN (LUMAZINE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,010,581120
Polymers993,16760
Non-polymers17,41460
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_645-z+1,x-1/2,-y+1/21
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
Buried area269020 Å2
ΔGint-793 kcal/mol
Surface area225340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)218.240, 218.240, 218.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Cell settingcubic
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.489, 0.837, -0.244), (-0.476, 0.49, 0.73), (0.731, -0.241, 0.638)-24.076, -65.495, 66.248
2given(-0.336, 0.877, 0.344), (0.065, -0.343, 0.937), (0.94, 0.337, 0.058)43.545, -132.629, 65.014
3given(-0.334, 0.057, 0.941), (0.876, -0.35, 0.332), (0.348, 0.935, 0.067)107.84, -107.572, -1.473
4given(0.494, -0.481, 0.724), (0.837, 0.49, -0.246), (-0.237, 0.727, 0.644)81.189, -26.598, -40.32
5given(0.241, 0.841, -0.484), (0.642, 0.236, 0.73), (0.728, -0.487, -0.483)3.689, -39.102, 214.343
6given(0.487, 0.724, 0.488), (0.728, -0.645, 0.231), (0.482, 0.243, -0.842)3.563, -105.775, 147.5
7given(0.737, -0.242, 0.631), (0.473, -0.482, -0.738), (0.482, 0.842, -0.241)-23.89, -65.751, 66.514
8given(0.637, -0.726, -0.258), (0.218, 0.492, -0.843), (0.739, 0.481, 0.472)-40.679, 26.775, 86.831
9given(0.328, -0.063, -0.943), (0.34, 0.939, 0.055), (0.882, -0.338, 0.329)-22.551, 43.661, 177.014
10given(0.00119, -0.00481, 0.99999), (-0.00046, -0.99999, -0.00481), (1, -0.00045, -0.00119)0.19335, 0.59639, -0.44819
11given(-0.2412, -0.8383, 0.4889), (0.7274, -0.4896, -0.4808), (0.6424, 0.2397, 0.7279)65.7575, 65.7683, -24.2099
12given(0.344, -0.877, -0.336), (0.937, 0.344, 0.061), (0.062, -0.336, 0.94)64.843, 132.416, 42.871
13given(0.936, -0.06, -0.347), (0.346, 0.341, 0.874), (0.066, -0.938, 0.34)-0.834, 108.751, 109.963
14given(0.728, 0.478, 0.491), (-0.244, -0.489, 0.837), (0.641, -0.73, -0.239)-40.096, 27.144, 80.985
15given(-0.487, -0.839, 0.242), (0.734, -0.243, 0.635), (-0.473, 0.487, 0.734)213.993, 39.059, 2.606
16given(0.488, -0.729, 0.48), (0.237, 0.64, 0.731), (-0.84, -0.243, 0.485)147.816, 106.702, 3.752
17given(0.6433, 0.2336, 0.7291), (-0.7269, 0.4853, 0.4858), (-0.2403, -0.8425, 0.482)65.133, 66.7963, -23.4074
18given(-0.238, 0.727, 0.645), (-0.841, -0.486, 0.237), (0.486, -0.486, 0.727)82.693, -26.435, -40.809
19given(-0.938, 0.062, 0.342), (0.06, -0.94, 0.335), (0.342, 0.334, 0.878)174.818, -42.908, -24.136

-
Components

#1: Protein
PROTEIN (LUMAZINE SYNTHASE) / E.C.2.5.1.9 / 6 / 7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE / DMRL SYNTHASE / RIBOFLAVIN SYNTHASE BETA CHAIN


Mass: 16552.789 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Organelle: CHLOROPLAST / Plasmid: PET-24A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9XH32, 6,7-dimethyl-8-ribityllumazine synthase
#2: Chemical
ChemComp-LMZ / 5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE


Mass: 290.230 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C9H14N4O7

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1 M TRIS-HCL PH 7.6, 17 % PEG 1500, 5 % PEG 400, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris-HCl1reservoir
217 %PEG15001reservoir
35 %PEG4001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.958
DetectorType: MARRESEARCH / Detector: MAR / Date: Mar 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.958 Å / Relative weight: 1
ReflectionResolution: 3.3→25 Å / Num. obs: 52248 / % possible obs: 98.3 % / Biso Wilson estimate: 94 Å2 / Rsym value: 11.1 / Net I/σ(I): 12.1
Reflection shellResolution: 3.3→3.36 Å / Mean I/σ(I) obs: 3.9 / Rsym value: 33.8 / % possible all: 98.3
Reflection
*PLUS
Num. measured all: 801553 / Rmerge(I) obs: 0.111
Reflection shell
*PLUS
% possible obs: 98.3 % / Rmerge(I) obs: 0.338

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RVV

1rvv


Resolution: 3.3→12 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.326 2565 5.02 %SHELLS
Rwork0.31 ---
obs0.31 50119 --
Displacement parametersBiso mean: 44.7 Å2
Refinement stepCycle: LAST / Resolution: 3.3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23100 0 400 0 23500
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.713
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.414
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINTS+RESTRAINTS
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2INI.PARINI.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.414

+
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