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- PDB-2b98: Crystal Structure of an archaeal pentameric riboflavin synthase -

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Basic information

Entry
Database: PDB / ID: 2b98
TitleCrystal Structure of an archaeal pentameric riboflavin synthase
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
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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


Theoretical massNumber of molelcules
Total (without water)87,6235
Polymers87,6235
Non-polymers00
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11840 Å2
ΔGint-73 kcal/mol
Surface area29010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.773, 72.692, 72.698
Angle α, β, γ (deg.)68.48, 74.61, 74.90
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61A
71B
81C
91D
101E
111A
121B
131C
141D
151E

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLUGLUAA5 - 275 - 27
21VALVALGLUGLUBB5 - 275 - 27
31VALVALGLUGLUCC5 - 275 - 27
41VALVALGLUGLUDD5 - 275 - 27
51VALVALGLUGLUEE5 - 275 - 27
62ARGARGVALVALAA36 - 10036 - 100
72ARGARGVALVALBB36 - 10036 - 100
82ARGARGVALVALCC36 - 10036 - 100
92ARGARGVALVALDD36 - 10036 - 100
102ARGARGVALVALEE36 - 10036 - 100
113LYSLYSTHRTHRAA109 - 137109 - 137
123LYSLYSTHRTHRBB109 - 137109 - 137
133LYSLYSTHRTHRCC109 - 137109 - 137
143LYSLYSTHRTHRDD109 - 137109 - 137
153LYSLYSTHRTHREE109 - 137109 - 137
DetailsThe biological assembly is a pentamer.

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Components

#1: Protein
Riboflavin synthase /


Mass: 17524.590 Da / Num. of mol.: 5
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.22 Å3/Da / Density % sol: 44.62 %
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: Jul 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 32165

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.859 / SU B: 8.771 / SU ML: 0.216 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27564 1677 5.2 %RANDOM
Rwork0.20773 ---
all0.21131 ---
obs0.21131 30444 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.019 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0.16 Å2-0.32 Å2
2--0.57 Å2-1.27 Å2
3---1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5695 0 0 294 5989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215421
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.987324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.355718
X-RAY DIFFRACTIONr_chiral_restr0.0780.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023916
X-RAY DIFFRACTIONr_nbd_refined0.2240.23004
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2318
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.27
X-RAY DIFFRACTIONr_mcbond_it0.41.53588
X-RAY DIFFRACTIONr_mcangle_it0.75825704
X-RAY DIFFRACTIONr_scbond_it1.24531833
X-RAY DIFFRACTIONr_scangle_it1.9484.51620
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A468medium positional0.180.5
2B468medium positional0.190.5
3C468medium positional0.160.5
4D468medium positional0.190.5
5E468medium positional0.150.5
1A351loose positional0.335
2B351loose positional0.315
3C351loose positional0.265
4D351loose positional0.375
5E351loose positional0.345
1A468medium thermal0.442
2B468medium thermal0.452
3C468medium thermal0.442
4D468medium thermal0.412
5E468medium thermal0.422
1A351loose thermal1.2210
2B351loose thermal1.5110
3C351loose thermal1.4410
4D351loose thermal1.3310
5E351loose thermal1.3610
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.248 2235
obs-2235
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6485-0.22760.29720.9517-0.14980.55450.01210.0352-0.0984-0.06680.0233-0.0095-0.0147-0.0399-0.03550.0383-0.00250.00880.0474-0.00530.0172-2.1818-3.5726-20.8946
20.77110.10610.15270.7014-0.07380.6552-0.0027-0.0522-0.0672-0.04920.0065-0.01370.06150.0126-0.00380.04670.0048-0.00140.0082-0.00560.0508-1.7744-21.3829-2.7545
30.4113-0.06680.02360.51970.05960.90360.01390.0050.00390.009-0.00710.0165-0.0152-0.0052-0.00680.0237-0.00230.00120.0275-0.01890.0204-3.148414.802415.9109
40.45060.16-0.17370.8614-0.17340.69650.0312-0.073-0.06310.0227-0.0352-0.03450.0451-0.00760.00410.044-0.0069-0.02070.03930.01140.029-2.1287-9.441719.633
50.4798-0.0784-0.12510.66490.07660.56140.00380.0801-0.0093-0.03030.00330.0008-0.0009-0.0579-0.00710.03410.00650.00260.01570.00690.0325-2.981119.5137-9.0937
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1433 - 143
2X-RAY DIFFRACTION2BB2 - 1422 - 142
3X-RAY DIFFRACTION3CC3 - 1533 - 153
4X-RAY DIFFRACTION4DD3 - 1423 - 142
5X-RAY DIFFRACTION5EE2 - 1532 - 153

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