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- PDB-3a3g: Crystal structure of LumP complexed with 6,7-dimethyl-8-(1'-D-rib... -

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Basic information

Entry
Database: PDB / ID: 3a3g
TitleCrystal structure of LumP complexed with 6,7-dimethyl-8-(1'-D-ribityl) lumazine
ComponentsLumazine protein
KeywordsLUMINESCENT PROTEIN / luminous bacteria / lumazine protein / photobacterium
Function / homology
Function and homology information


riboflavin synthase activity / riboflavin biosynthetic process / nucleotide binding
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-DLZ / Lumazine protein
Similarity search - Component
Biological speciesPhotobacterium kishitanii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSato, Y.
CitationJournal: J.Bacteriol. / Year: 2009
Title: Crystal structures of the lumazine protein from Photobacterium kishitanii in complexes with the authentic chromophore, 6,7-dimethyl-8-(1'-D-ribityl) lumazine and its analogues, riboflavin and ...Title: Crystal structures of the lumazine protein from Photobacterium kishitanii in complexes with the authentic chromophore, 6,7-dimethyl-8-(1'-D-ribityl) lumazine and its analogues, riboflavin and FMN, at high resolution
Authors: Sato, Y. / Shimizu, S. / Ohtaki, A. / Noguchi, K. / Miyatake, H. / Dohmae, N. / Sasaki, S. / Odaka, M. / Yohda, M.
History
DepositionJun 12, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 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

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Assembly

Deposited unit
A: Lumazine protein
B: Lumazine protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4764
Polymers41,8232
Non-polymers6532
Water3,315184
1
A: Lumazine protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2382
Polymers20,9121
Non-polymers3261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lumazine protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2382
Polymers20,9121
Non-polymers3261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.689, 46.584, 161.587
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lumazine protein / LumP


Mass: 20911.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium kishitanii (bacteria) / Gene: luminous bacteria / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / References: UniProt: C4TPG1
#2: Chemical ChemComp-DLZ / 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol / 6,7-dimethyl-8-(1'-D-ribityl) lumazine


Mass: 326.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H18N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE EXTERNAL REGION OF LUMP GENE FROM P. KISHITANII IS NOT CLEAR, THEREFORE, DEPOSITORS DESIGNED ...THE EXTERNAL REGION OF LUMP GENE FROM P. KISHITANII IS NOT CLEAR, THEREFORE, DEPOSITORS DESIGNED THESE PRIMER REGION TO AMPLIFY THE GENE BASED ON INTERNAL REGION OF LUMP GENE FROM P. PHOSPHOREUM. THIS SEQUENCE WAS COMPLETELY MATCH LUMP GENE FROM P. PHOSPHOREUM.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20%(w/v) PEG 4000, 0.2M MgCl2, 100mM Tris-HCl pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→44.766 Å / Num. obs: 23305 / % possible obs: 99.7563 %

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.766 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.886 / SU B: 4.062 / SU ML: 0.116 / Isotropic thermal model: PDB ENTRY 3DDY / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 1255 5.1 %RANDOM
Rwork0.19474 ---
obs0.19768 23305 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.594 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→44.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2752 0 46 185 2983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222820
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.9893812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1725353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95226.417120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03515527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.7671510
X-RAY DIFFRACTIONr_chiral_restr0.1530.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022029
X-RAY DIFFRACTIONr_nbd_refined0.2220.21185
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21880
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.220
X-RAY DIFFRACTIONr_mcbond_it1.2171.51808
X-RAY DIFFRACTIONr_mcangle_it2.0722864
X-RAY DIFFRACTIONr_scbond_it2.86131177
X-RAY DIFFRACTIONr_scangle_it4.7484.5948
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 90 -
Rwork0.208 1651 -
obs--98.03 %

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