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- PDB-2d38: The Crystal Structure of Flavin Reductase HpaC complexed with NADP+ -

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Basic information

Entry
Database: PDB / ID: 2d38
TitleThe Crystal Structure of Flavin Reductase HpaC complexed with NADP+
Componentshypothetical NADH-dependent FMN oxidoreductase
KeywordsOXIDOREDUCTASE / flavin reductase
Function / homology
Function and homology information


phenol 2-monooxygenase (NADPH) / phenol 2-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
FLAVIN MONONUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / : / Phenol hydroxylase small component
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsOkai, M. / Kudo, N. / Lee, W.C. / Kamo, M. / Nagata, K. / Tanokura, M.
CitationJournal: Biochemistry / Year: 2006
Title: Crystal structures of the short-chain flavin reductase HpaC from Sulfolobus tokodaii strain 7 in its three states: NAD(P)(+)(-)free, NAD(+)(-)bound, and NADP(+)(-)bound
Authors: Okai, M. / Kudo, N. / Lee, W.C. / Kamo, M. / Nagata, K. / Tanokura, M.
History
DepositionSep 26, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2006Provider: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: hypothetical NADH-dependent FMN oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3573
Polymers20,1571
Non-polymers1,2002
Water1,00956
1
A: hypothetical NADH-dependent FMN oxidoreductase
hetero molecules

A: hypothetical NADH-dependent FMN oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7146
Polymers40,3142
Non-polymers2,3994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area8600 Å2
ΔGint-54 kcal/mol
Surface area12250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.617, 86.617, 49.122
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein hypothetical NADH-dependent FMN oxidoreductase / NADH:flavin reductase


Mass: 20157.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: str. 7 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: GenBank: 15920953, UniProt: Q974C9*PLUS, EC: 1.6.8.-
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ammonium sulfate, iso-propanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.984 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 2, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 13622 / % possible obs: 99.1 %
Reflection shellResolution: 2.05→2.12 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.903 / SU B: 3.941 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24592 690 5.1 %RANDOM
Rwork0.20388 ---
obs0.20593 12795 99.21 %-
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: 24.417 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20 Å2
2--0.05 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1257 0 79 56 1392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221372
X-RAY DIFFRACTIONr_bond_other_d0.0580.021206
X-RAY DIFFRACTIONr_angle_refined_deg1.3422.0331871
X-RAY DIFFRACTIONr_angle_other_deg1.75232811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2225155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021448
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02273
X-RAY DIFFRACTIONr_nbd_refined0.1870.2213
X-RAY DIFFRACTIONr_nbd_other0.2490.21340
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.2741
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7741.5776
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3921261
X-RAY DIFFRACTIONr_scbond_it1.4823596
X-RAY DIFFRACTIONr_scangle_it2.4624.5610
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.051→2.103 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.302 53
Rwork0.213 925

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