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- PDB-1zis: Recombinant Lumazine synthase (hexagonal form) -

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Basic information

Entry
Database: PDB / ID: 1zis
TitleRecombinant Lumazine synthase (hexagonal form)
Components6,7-dimethyl-8-ribityllumazine synthase
KeywordsTRANSFERASE
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 / cytoplasm / cytosol
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-INI / PHOSPHATE ION / 6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLopez-Jaramillo, F.J.
Citation
Journal: To be Published
Title: Crystal structure of recombinant Lumazine synthase (hexagonal form)
Authors: Lopez-Jaramillo, F.J.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Studies on the Lumazine Synthase/Riboflavin Synthase Complex of Bacillus subtilis: Crystal Structure Analysis of Reconstituted, Icosahedral b-subunit Capsids with Bound Substrate Analogue ...Title: Studies on the Lumazine Synthase/Riboflavin Synthase Complex of Bacillus subtilis: Crystal Structure Analysis of Reconstituted, Icosahedral b-subunit Capsids with Bound Substrate Analogue Inhibitor at 2.4 A Resolution
Authors: Ritsert, K. / Huber, R. / Turk, D. / Ladenstein, R. / Scmidt-Base, K. / Bacher, A.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Heavy Riboflavin Synthase from Bacillus subtilis: Crystal Structure Analysis of the Icosahedral b60 Capsid at 3.3 A Resolution
Authors: Ladenstein, R. / Schneider, M. / Huber, R. / Bartunik, H.-D. / Wilson, K. / Schott, K. / Bacher, A.
#3: Journal: J.Biol.Chem. / Year: 1990
Title: The Lumazine Synthase-Riboflavin Synthase Complex of Bacillus subtilis. Crystallization of Reconstituted Icosahedral b-subunit Capsids
Authors: Schott, K. / Ladenstein, R. / Konig, A. / Bacher, A.
History
DepositionApr 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 16, 2013Group: Other
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Aug 23, 2023Group: Data collection / Database references ...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 / 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: 6,7-dimethyl-8-ribityllumazine synthase
B: 6,7-dimethyl-8-ribityllumazine synthase
C: 6,7-dimethyl-8-ribityllumazine synthase
D: 6,7-dimethyl-8-ribityllumazine synthase
E: 6,7-dimethyl-8-ribityllumazine synthase
F: 6,7-dimethyl-8-ribityllumazine synthase
G: 6,7-dimethyl-8-ribityllumazine synthase
H: 6,7-dimethyl-8-ribityllumazine synthase
I: 6,7-dimethyl-8-ribityllumazine synthase
J: 6,7-dimethyl-8-ribityllumazine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,03830
Polymers163,02610
Non-polymers4,01220
Water00
1
A: 6,7-dimethyl-8-ribityllumazine synthase
B: 6,7-dimethyl-8-ribityllumazine synthase
C: 6,7-dimethyl-8-ribityllumazine synthase
D: 6,7-dimethyl-8-ribityllumazine synthase
E: 6,7-dimethyl-8-ribityllumazine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,51915
Polymers81,5135
Non-polymers2,00610
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14520 Å2
ΔGint-100 kcal/mol
Surface area27860 Å2
MethodPISA
2
F: 6,7-dimethyl-8-ribityllumazine synthase
G: 6,7-dimethyl-8-ribityllumazine synthase
H: 6,7-dimethyl-8-ribityllumazine synthase
I: 6,7-dimethyl-8-ribityllumazine synthase
J: 6,7-dimethyl-8-ribityllumazine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,51915
Polymers81,5135
Non-polymers2,00610
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18240 Å2
ΔGint-125 kcal/mol
Surface area28750 Å2
MethodPISA
3
F: 6,7-dimethyl-8-ribityllumazine synthase
G: 6,7-dimethyl-8-ribityllumazine synthase
H: 6,7-dimethyl-8-ribityllumazine synthase
I: 6,7-dimethyl-8-ribityllumazine synthase
J: 6,7-dimethyl-8-ribityllumazine synthase
hetero molecules
x 6
A: 6,7-dimethyl-8-ribityllumazine synthase
B: 6,7-dimethyl-8-ribityllumazine synthase
C: 6,7-dimethyl-8-ribityllumazine synthase
D: 6,7-dimethyl-8-ribityllumazine synthase
E: 6,7-dimethyl-8-ribityllumazine synthase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)1,002,226180
Polymers978,15460
Non-polymers24,072120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation9_556-x,-x+y,-z+11
crystal symmetry operation4_665-x+1,-y+1,z+1/21
crystal symmetry operation5_455y-1,-x+y,z+1/21
crystal symmetry operation6_545x-y,x-1,z+1/21
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_545-x+y,y-1,-z+1/21
crystal symmetry operation12_455x-1,x-y,-z+1/21
Buried area280630 Å2
ΔGint-1600 kcal/mol
Surface area255540 Å2
MethodPISA
4
A: 6,7-dimethyl-8-ribityllumazine synthase
B: 6,7-dimethyl-8-ribityllumazine synthase
C: 6,7-dimethyl-8-ribityllumazine synthase
D: 6,7-dimethyl-8-ribityllumazine synthase
E: 6,7-dimethyl-8-ribityllumazine synthase
hetero molecules
x 6
F: 6,7-dimethyl-8-ribityllumazine synthase
G: 6,7-dimethyl-8-ribityllumazine synthase
H: 6,7-dimethyl-8-ribityllumazine synthase
I: 6,7-dimethyl-8-ribityllumazine synthase
J: 6,7-dimethyl-8-ribityllumazine synthase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)1,002,226180
Polymers978,15460
Non-polymers24,072120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
crystal symmetry operation9_765-x+2,-x+y+1,-z1
crystal symmetry operation4_664-x+1,-y+1,z-1/21
crystal symmetry operation5_664y+1,-x+y+1,z-1/21
crystal symmetry operation6_664x-y+1,x+1,z-1/21
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_665-x+y+1,y+1,-z+1/21
crystal symmetry operation12_665x+1,x-y+1,-z+1/21
Buried area280670 Å2
ΔGint-1601 kcal/mol
Surface area255500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.690, 153.690, 296.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein
6,7-dimethyl-8-ribityllumazine synthase / DMRL synthase / Lumazine synthase / Riboflavin synthase beta chain


Mass: 16302.567 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ribH / Plasmid: P602-22 / Production host: Bacillus subtilis (bacteria) / Strain (production host): BR151
References: UniProt: P11998, 6,7-dimethyl-8-ribityllumazine synthase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-INI / 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE


Mass: 306.229 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C9H14N4O8

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.7
Details: Phosphate buffer, pH 8.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jun 22, 2004 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→19.6 Å / Num. obs: 40931 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 44.616 Å2 / Limit h max: 45 / Limit h min: 0 / Limit k max: 26 / Limit k min: 0 / Limit l max: 102 / Limit l min: 0 / Observed criterion F max: 7253072.27 / Observed criterion F min: 83.39 / Rmerge(I) obs: 0.085 / Rsym value: 0.073 / Net I/σ(I): 17.59
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 8.38 / Num. unique all: 3377 / Rsym value: 0.15 / % possible all: 77.1

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Processing

Software
NameVersionClassificationNB
CNS1refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pentamer from 1RVV

1rvv


Resolution: 2.9→10 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 4016 10 %RANDOM
Rwork0.206 ---
all-45255 --
obs-39996 88.4 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 24.9564 Å2 / ksol: 0.327727 e/Å3
Displacement parametersBiso max: 194.39 Å2 / Biso mean: 44.29 Å2 / Biso min: 5.71 Å2
Baniso -1Baniso -2Baniso -3
1--7.33 Å21.5 Å20 Å2
2---7.33 Å20 Å2
3---14.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.47 Å
Luzzati d res high-2.9
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11440 0 260 0 11700
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg22.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.78
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTIONprotein_rep.paramprotein.topion.param
X-RAY DIFFRACTIONion.topini.parini.top

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