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- PDB-1c41: CRYSTAL STRUCTURES OF A PENTAMERIC FUNGAL AND AN ICOSAHEDRAL PLAN... -

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Basic information

Entry
Database: PDB / ID: 1c41
TitleCRYSTAL STRUCTURES OF A PENTAMERIC FUNGAL AND AN ICOSAHEDRAL PLANT LUMAZINE SYNTHASE REVEALS THE STRUCTURAL BASIS FOR DIFFERENCES IN ASSEMBLY
ComponentsLUMAZINE 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 / mitochondrial intermembrane space
Similarity search - Function
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
Similarity search - Component
Biological speciesMagnaporthe grisea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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
DepositionAug 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 16, 2013Group: Structure summary
Revision 1.4Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Aug 9, 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)215,76240
Polymers210,93910
Non-polymers4,82430
Water18010
1
A: LUMAZINE SYNTHASE
B: LUMAZINE SYNTHASE
C: LUMAZINE SYNTHASE
D: LUMAZINE SYNTHASE
E: LUMAZINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,88120
Polymers105,4695
Non-polymers2,41215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21390 Å2
ΔGint-208 kcal/mol
Surface area26070 Å2
MethodPISA
2
F: LUMAZINE SYNTHASE
G: LUMAZINE SYNTHASE
H: LUMAZINE SYNTHASE
I: LUMAZINE SYNTHASE
J: LUMAZINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,88120
Polymers105,4695
Non-polymers2,41215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21360 Å2
ΔGint-208 kcal/mol
Surface area26070 Å2
MethodPISA
3
A: LUMAZINE SYNTHASE
B: LUMAZINE SYNTHASE
C: LUMAZINE SYNTHASE
D: LUMAZINE SYNTHASE
E: LUMAZINE SYNTHASE
hetero molecules

F: LUMAZINE SYNTHASE
G: LUMAZINE SYNTHASE
H: LUMAZINE SYNTHASE
I: LUMAZINE SYNTHASE
J: LUMAZINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,76240
Polymers210,93910
Non-polymers4,82430
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area45750 Å2
ΔGint-430 kcal/mol
Surface area49140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.800, 124.700, 141.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9975, -0.0587, -0.0386), (-0.0189, 0.3058, -0.9519), (0.0677, 0.9503, 0.304)-3.4284, -46.9073, 39.8449
2given(0.995, -0.102, 0.013), (-0.075, -0.804, -0.59), (0.071, 0.586, -0.807)-3.376, -23.81, 96.539
3given(0.9944, -0.0708, 0.078), (-0.1033, -0.8016, 0.5889), (0.0208, -0.5937, -0.8044)-0.7402, 37.6131, 91.9088
4given(0.9976, -0.0102, 0.0682), (-0.0612, 0.3226, 0.9445), (-0.0316, -0.9465, 0.3212)1.8649, 51.6663, 31.9699
5given(0.995, 0.032, 0.09), (-0.05, -0.627, 0.778), (0.081, -0.778, -0.622)48.106, 106.847, 46.701
6given(0.994, 0.09, 0.062), (-0.101, 0.544, 0.833), (0.041, -0.834, 0.55)50.424, 105.462, -14.491
7given(0.9966, 0.082, -0.0033), (-0.0799, 0.961, -0.2647), (-0.0185, 0.2641, 0.9643)53.417, 46.6455, -32.0285
8given(0.9994, 0.0211, -0.0259), (-0.027, 0.0533, -0.9982), (-0.0197, 0.9984, 0.0539)53.4146, 11.6551, 18.0235
9given(0.9992, -0.0122, 0.0377), (0.0019, -0.9357, -0.3527), (0.0396, 0.3525, -0.935)50.0842, 49.0867, 67.1495

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Components

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


Mass: 21093.871 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe grisea (fungus) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UVT8, 6,7-dimethyl-8-ribityllumazine synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-LMZ / 5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE


Mass: 290.230 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C9H14N4O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.2 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
2100 mMMES1reservoir
327 %mPEG50001reservoir
4200 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.958
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.958 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 31842 / % possible obs: 99 % / Redundancy: 16.9 % / Rsym value: 0.136 / Net I/σ(I): 12
Reflection shellResolution: 3.1→3.17 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.396 / % possible all: 91.5
Reflection
*PLUS
Num. measured all: 539917 / Rmerge(I) obs: 0.136
Reflection shell
*PLUS
% possible obs: 91.5 % / Rmerge(I) obs: 0.396

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RVV

1rvv


Resolution: 3.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 -4.9 %RANDOM
Rwork0.248 ---
obs0.248 31795 98.1 %-
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1--6.3 Å20 Å20 Å2
2--13.9 Å20 Å2
3----7.6 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12430 0 300 10 12740
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: STRICT
LS refinement shellResolution: 3.1→3.13 Å / Total num. of bins used: 32
RfactorNum. reflection% reflection
Rfree0.347 47 4.9 %
Rwork0.359 727 -
obs--81 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAINI.TOP
X-RAY DIFFRACTION4INI.PARION.TOP

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