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- PDB-2b99: Crystal Structure of an archaeal pentameric riboflavin synthase C... -

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Basic information

Entry
Database: PDB / ID: 2b99
TitleCrystal Structure of an archaeal pentameric riboflavin synthase Complex with a Substrate analog inhibitor
ComponentsRiboflavin synthase
KeywordsTRANSFERASE / lumazine riboflavin
Function / homology
Function and homology information


riboflavin synthase / riboflavin synthase activity / riboflavin synthase complex / riboflavin biosynthetic process
Similarity search - Function
Riboflavin synthase, archaeal / Lumazine/riboflavin 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
6,7-DIOXO-5H-8-RIBITYLAMINOLUMAZINE / Riboflavin synthase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsRamsperger, A. / Augustin, M. / Schott, A.K. / Gerhardt, S. / Krojer, T. / Eisenreich, W. / Illarionov, B. / Cushman, M. / Bacher, A. / Huber, R. / Fischer, M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of an Archaeal Pentameric Riboflavin Synthase in Complex with a Substrate Analog Inhibitor: stereochemical implications
Authors: Ramsperger, A. / Augustin, M. / Schott, A.K. / Gerhardt, S. / Krojer, T. / Eisenreich, W. / Illarionov, B. / Cushman, M. / Bacher, A. / Huber, R. / Fischer, M.
History
DepositionOct 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Riboflavin synthase
B: Riboflavin synthase
C: Riboflavin synthase
D: Riboflavin synthase
E: Riboflavin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,92515
Polymers87,6235
Non-polymers3,30310
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18860 Å2
ΔGint-56 kcal/mol
Surface area27130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.940, 72.912, 72.782
Angle α, β, γ (deg.)68.50, 74.39, 74.53
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a pentamer.

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Components

#1: Protein
Riboflavin synthase


Mass: 17524.590 Da / Num. of mol.: 5 / Fragment: riboflavin synthase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: ribC / Plasmid: pNCO113 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58584, riboflavin synthase
#2: Chemical
ChemComp-RDL / 6,7-DIOXO-5H-8-RIBITYLAMINOLUMAZINE


Mass: 330.251 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C11H14N4O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES, pH 7.0, and 40% MPD., VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 34797 / Biso Wilson estimate: 26.3 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→19.92 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 958644.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1741 5 %RANDOM
Rwork0.258 ---
all0.258 ---
obs0.258 34789 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.3065 Å2 / ksol: 0.32196 e/Å3
Displacement parametersBiso mean: 30.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.14 Å2-1.32 Å2-2.25 Å2
2--6.78 Å2-3.55 Å2
3----2.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.22→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5750 0 230 207 6187
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
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: CONSTR
LS refinement shellResolution: 2.22→2.36 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 154 2.9 %
Rwork0.284 5200 -
obs--86 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramrdl.topo
X-RAY DIFFRACTION3rdl.parawater.top

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