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- PDB-1rvv: SYNTHASE/RIBOFLAVIN SYNTHASE COMPLEX OF BACILLUS SUBTILIS -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1rvv
TitleSYNTHASE/RIBOFLAVIN SYNTHASE COMPLEX OF BACILLUS SUBTILIS
ComponentsRIBOFLAVIN SYNTHASE
KeywordsRIBOFLAVIN SYNTHASE / TRANSFERASE / FLAVOPROTEIN
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 / 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 / Resolution: 2.4 Å
AuthorsRitsert, K. / Huber, R. / Turk, D. / Ladenstein, R. / Schmidt-Baese, K. / Bacher, A.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: Studies on the lumazine synthase/riboflavin synthase complex of Bacillus subtilis: crystal structure analysis of reconstituted, icosahedral beta-subunit capsids with bound substrate analogue ...Title: Studies on the lumazine synthase/riboflavin synthase complex of Bacillus subtilis: crystal structure analysis of reconstituted, icosahedral beta-subunit capsids with bound substrate analogue inhibitor at 2.4 A resolution.
Authors: Ritsert, K. / Huber, R. / Turk, D. / Ladenstein, R. / Schmidt-Base, K. / Bacher, A.
History
DepositionOct 25, 1995Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: RIBOFLAVIN SYNTHASE
B: RIBOFLAVIN SYNTHASE
C: RIBOFLAVIN SYNTHASE
D: RIBOFLAVIN SYNTHASE
E: RIBOFLAVIN SYNTHASE
F: RIBOFLAVIN SYNTHASE
G: RIBOFLAVIN SYNTHASE
H: RIBOFLAVIN SYNTHASE
I: RIBOFLAVIN SYNTHASE
J: RIBOFLAVIN SYNTHASE
K: RIBOFLAVIN SYNTHASE
L: RIBOFLAVIN SYNTHASE
M: RIBOFLAVIN SYNTHASE
N: RIBOFLAVIN SYNTHASE
O: RIBOFLAVIN SYNTHASE
P: RIBOFLAVIN SYNTHASE
Q: RIBOFLAVIN SYNTHASE
R: RIBOFLAVIN SYNTHASE
S: RIBOFLAVIN SYNTHASE
T: RIBOFLAVIN SYNTHASE
U: RIBOFLAVIN SYNTHASE
V: RIBOFLAVIN SYNTHASE
W: RIBOFLAVIN SYNTHASE
X: RIBOFLAVIN SYNTHASE
Y: RIBOFLAVIN SYNTHASE
Z: RIBOFLAVIN SYNTHASE
1: RIBOFLAVIN SYNTHASE
2: RIBOFLAVIN SYNTHASE
3: RIBOFLAVIN SYNTHASE
4: RIBOFLAVIN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)501,11390
Polymers489,07730
Non-polymers12,03660
Water18,9161050
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RIBOFLAVIN SYNTHASE
B: RIBOFLAVIN SYNTHASE
C: RIBOFLAVIN SYNTHASE
D: RIBOFLAVIN SYNTHASE
E: RIBOFLAVIN SYNTHASE
F: RIBOFLAVIN SYNTHASE
G: RIBOFLAVIN SYNTHASE
H: RIBOFLAVIN SYNTHASE
I: RIBOFLAVIN SYNTHASE
J: RIBOFLAVIN SYNTHASE
K: RIBOFLAVIN SYNTHASE
L: RIBOFLAVIN SYNTHASE
M: RIBOFLAVIN SYNTHASE
N: RIBOFLAVIN SYNTHASE
O: RIBOFLAVIN SYNTHASE
P: RIBOFLAVIN SYNTHASE
Q: RIBOFLAVIN SYNTHASE
R: RIBOFLAVIN SYNTHASE
S: RIBOFLAVIN SYNTHASE
T: RIBOFLAVIN SYNTHASE
U: RIBOFLAVIN SYNTHASE
V: RIBOFLAVIN SYNTHASE
W: RIBOFLAVIN SYNTHASE
X: RIBOFLAVIN SYNTHASE
Y: RIBOFLAVIN SYNTHASE
Z: RIBOFLAVIN SYNTHASE
1: RIBOFLAVIN SYNTHASE
2: RIBOFLAVIN SYNTHASE
3: RIBOFLAVIN SYNTHASE
4: RIBOFLAVIN SYNTHASE
hetero molecules

A: RIBOFLAVIN SYNTHASE
B: RIBOFLAVIN SYNTHASE
C: RIBOFLAVIN SYNTHASE
D: RIBOFLAVIN SYNTHASE
E: RIBOFLAVIN SYNTHASE
F: RIBOFLAVIN SYNTHASE
G: RIBOFLAVIN SYNTHASE
H: RIBOFLAVIN SYNTHASE
I: RIBOFLAVIN SYNTHASE
J: RIBOFLAVIN SYNTHASE
K: RIBOFLAVIN SYNTHASE
L: RIBOFLAVIN SYNTHASE
M: RIBOFLAVIN SYNTHASE
N: RIBOFLAVIN SYNTHASE
O: RIBOFLAVIN SYNTHASE
P: RIBOFLAVIN SYNTHASE
Q: RIBOFLAVIN SYNTHASE
R: RIBOFLAVIN SYNTHASE
S: RIBOFLAVIN SYNTHASE
T: RIBOFLAVIN SYNTHASE
U: RIBOFLAVIN SYNTHASE
V: RIBOFLAVIN SYNTHASE
W: RIBOFLAVIN SYNTHASE
X: RIBOFLAVIN SYNTHASE
Y: RIBOFLAVIN SYNTHASE
Z: RIBOFLAVIN SYNTHASE
1: RIBOFLAVIN SYNTHASE
2: RIBOFLAVIN SYNTHASE
3: RIBOFLAVIN SYNTHASE
4: RIBOFLAVIN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,002,226180
Polymers978,15460
Non-polymers24,072120
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area265510 Å2
ΔGint-1569 kcal/mol
Surface area243120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)235.900, 192.600, 168.600
Angle α, β, γ (deg.)90.00, 134.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ...
RIBOFLAVIN SYNTHASE


Mass: 16302.567 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: P11998
#2: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 30 / 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.: 30 / Source method: obtained synthetically / Formula: C9H14N4O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1050 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal grow
*PLUS
pH: 8.7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-8 mg/mlprotein1drop
20.8 Msodium/potassium phosphate1drop
31 mM5-nitro-6-ribitylamino-2,4(1H,3H)-pyrimidinedione1drop
41.55 Msodium/potassium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.4 Å / Observed criterion σ(I): 2
Reflection
*PLUS
Num. obs: 122010 / % possible obs: 51.2 % / Num. measured all: 18350500 / Rmerge(I) obs: 0.126

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.237 / Rfactor obs: 0.237 / Highest resolution: 2.4 Å
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34320 0 780 1050 36150
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 100092
Solvent computation
*PLUS
Displacement parameters
*PLUS

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