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

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Basic information

Entry
Database: PDB / ID: 1wgb
TitleCrystal structure of a probable flavoprotein from Thermus thermophilus HB8
Componentsprobable flavoprotein
KeywordsOXIDOREDUCTASE / flavoprotein / HB8 / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / monooxygenase 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
Probable nitrilotriacetate monooxygenase component B
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsImagawa, T. / Tsuge, H. / Utsunomiya, H. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of a probable flavoprotein from Thermus thermophilus HB8
Authors: Imagawa, T. / Tsuge, H. / Utsunomiya, H. / Yokoyama, S. / Kuramitsu, S.
History
DepositionMay 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: probable flavoprotein


Theoretical massNumber of molelcules
Total (without water)17,8911
Polymers17,8911
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: probable flavoprotein

A: probable flavoprotein


Theoretical massNumber of molelcules
Total (without water)35,7822
Polymers35,7822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4610 Å2
ΔGint-41 kcal/mol
Surface area12980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.780, 63.780, 80.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-283-

HOH

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Components

#1: Protein probable flavoprotein


Mass: 17890.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q72LK7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.22 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97923, 0.9000, 0.97954
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979231
20.91
30.979541
ReflectionResolution: 1.9→34 Å / Num. all: 13607 / Num. obs: 13607 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.85 % / Rmerge(I) obs: 0.038
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 9.09 % / Rmerge(I) obs: 0.049 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CrystalClear(MSC/RIGAKU)data reduction
SOLVEphasing
CNSrefinement
CrystalClear(MSC/RIGAKU)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→34 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 1212 -RANDOM
Rwork0.211 ---
obs0.211 11708 99.6 %-
all-11757 --
Refinement stepCycle: LAST / Resolution: 2→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1255 0 0 129 1384
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005542
X-RAY DIFFRACTIONc_angle_deg1.2393

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