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- PDB-1yoa: Crystal structure of a probable flavoprotein from Thermus thermop... -

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Basic information

Entry
Database: PDB / ID: 1yoa
TitleCrystal structure of a probable flavoprotein from Thermus thermophilus HB8
Componentsputative flavoprotein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / flavoprotein / HB8 / FAD / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


riboflavin reductase (NADPH) activity / FMN binding
Similarity search - Function
: / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / Flavoprotein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsImagawa, T. / Tsuge, H. / Sugimoto, Y. / Utsunomiya, H. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Crystal structure of a flavoenzyme TTHA0420 from Thermus thermophilus HB8
Authors: Imagawa, T. / Tsuge, H. / Sugimoto, Y. / Utsunomiya, H. / Yokoyama, S. / Kuramitsu, S.
History
DepositionJan 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / 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 / 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: putative flavoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9923
Polymers17,7501
Non-polymers1,2422
Water1,20767
1
A: putative flavoprotein
hetero molecules

A: putative flavoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9846
Polymers35,5012
Non-polymers2,4844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation43_555-x+1/2,-z+1/2,-y+1/21
Buried area8130 Å2
ΔGint-63 kcal/mol
Surface area12260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.966, 132.966, 132.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein putative flavoprotein


Mass: 17750.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SL73
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG400, ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→95.35 Å / Num. all: 16153 / Num. obs: 16153 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 41.7 % / Rsym value: 0.11
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 43.2 % / Num. unique all: 1568 / Rsym value: 0.292 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→35.54 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.588 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.147 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22761 813 5 %RANDOM
Rwork0.19989 ---
all0.201 16159 --
obs0.2013 15335 99.96 %-
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: 20.486 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1255 0 84 67 1406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211381
X-RAY DIFFRACTIONr_bond_other_d0.0020.021216
X-RAY DIFFRACTIONr_angle_refined_deg1.512.0311894
X-RAY DIFFRACTIONr_angle_other_deg0.8532824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9345158
X-RAY DIFFRACTIONr_chiral_restr0.0990.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021473
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02267
X-RAY DIFFRACTIONr_nbd_refined0.1960.2214
X-RAY DIFFRACTIONr_nbd_other0.2490.21339
X-RAY DIFFRACTIONr_nbtor_other0.0850.2811
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.274
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.380.28
X-RAY DIFFRACTIONr_mcbond_it0.8611.5791
X-RAY DIFFRACTIONr_mcangle_it1.63621271
X-RAY DIFFRACTIONr_scbond_it2.623590
X-RAY DIFFRACTIONr_scangle_it4.3234.5623
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.285 73
Rwork0.194 1088

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