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- PDB-1c2y: CRYSTAL STRUCTURES OF A PENTAMERIC FUNGAL AND AN ICOSAHEDRAL PLAN... -

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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 / cytoplasm
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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