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- PDB-1kzl: Riboflavin Synthase from S.pombe bound to Carboxyethyllumazine -

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Basic information

Entry
Database: PDB / ID: 1kzl
TitleRiboflavin Synthase from S.pombe bound to Carboxyethyllumazine
ComponentsRiboflavin Synthase
KeywordsTRANSFERASE / biosynthesis of riboflavin / riboflavin synthase / Schizosaccharomyces pombe / ligand binding
Function / homology
Function and homology information


riboflavin synthase / riboflavin synthase activity / riboflavin biosynthetic process / nucleus / cytosol
Similarity search - Function
Lumazine-binding protein / Lumazine-binding domain / Lumazine binding domain / Riboflavin synthase alpha chain lumazine-binding repeat profile. / Elongation Factor Tu (Ef-tu); domain 3 - #20 / ATP synthase subunit alpha, N-terminal domain-like superfamily / Elongation Factor Tu (Ef-tu); domain 3 / Riboflavin synthase-like beta-barrel / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-CRM / : / Riboflavin synthase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsGerhardt, S. / Schott, A.K. / Kairies, N. / Cushman, M. / Illarionov, B. / Eisenreich, W. / Bacher, A. / Huber, R. / Steinbacher, S. / Fischer, M.
CitationJournal: STRUCTURE / Year: 2002
Title: Studies on the Reaction Mechanism of Riboflavin Synthase; X-Ray Crystal Structure of a Complex with 6-Carboxyethyl-7-Oxo-8-Ribityllumazine
Authors: Gerhardt, S. / Schott, A.K. / Kairies, N. / Cushman, M. / Illarionov, B. / Eisenreich, W. / Bacher, A. / Huber, R. / Steinbacher, S. / Fischer, M.
History
DepositionFeb 7, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Riboflavin Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8604
Polymers22,8871
Non-polymers9733
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.485, 70.485, 92.952
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsIn contrast to the homotrimeric solution state of native riboflavin synthase from S. pombe. But this structure is monomeric in its crystal structure.

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Components

#1: Protein Riboflavin Synthase / riboflavin synthase alpha chain


Mass: 22887.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: pNCO113 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y7P0, riboflavin synthase
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-CRM / 3-[8-((2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL)-2,4,7-TRIOXO-1,3,8-TRIHYDROPTERIDIN-6-YL]PROPANOIC ACID / CARBOXYETHYLLUMAZINE


Mass: 386.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N4O9
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: bicine, 2-methyl-2,4-pentanediol, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MBicine1reservoirpH9.0
265 %(v/v)MPD1reservoir
39 mg/mlenzyme1drop
420 mMTris-HCl1droppH7.0
5100 mM1dropKCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.010, 1.000, 0.9499
DetectorType: MARRESEARCH / Detector: CCD / Date: May 14, 2001
RadiationMonochromator: NULL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.011
211
30.94991
ReflectionResolution: 2.1→19.881 Å / Num. all: 15304 / Num. obs: 15097 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.14 Å / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 28494 / % possible obs: 94.5 % / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
% possible obs: 95.3 % / Rmerge(I) obs: 0.265

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→19.881 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2205 1530 RANDOM
Rwork0.1852 --
all0.189 15304 -
obs0.189 15097 -
Refinement stepCycle: LAST / Resolution: 2.1→19.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 55 121 1733
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005931
X-RAY DIFFRACTIONc_angle_deg1.23943
Refinement
*PLUS
Lowest resolution: 19.88 Å / % reflection Rfree: 10 % / Rfactor all: 0.189 / Rfactor obs: 0.189 / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.24

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