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- PDB-3u7r: FerB - flavoenzyme NAD(P)H:(acceptor) oxidoreductase (FerB) from ... -

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Basic information

Entry
Database: PDB / ID: 3u7r
TitleFerB - flavoenzyme NAD(P)H:(acceptor) oxidoreductase (FerB) from Paracoccus denitrificans
ComponentsNADPH-dependent FMN reductase
KeywordsOXIDOREDUCTASE / alpha/beta twisted open-sheet / lavoprotein / quinone reductase
Function / homology
Function and homology information


FMN binding / oxidoreductase activity / cytosol
Similarity search - Function
: / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FNR / NADPH-dependent FMN reductase
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsMarek, J. / Klumpler, T. / Sedlacek, V. / Kucera, I.
CitationJournal: Plos One / Year: 2014
Title: The Structural and Functional Basis of Catalysis Mediated by NAD(P)H:acceptor Oxidoreductase (FerB) of Paracoccus denitrificans.
Authors: Sedlacek, V. / Klumpler, T. / Marek, J. / Kucera, I.
History
DepositionOct 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references / Derived calculations
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: NADPH-dependent FMN reductase
B: NADPH-dependent FMN reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6285
Polymers43,2972
Non-polymers1,3313
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-16 kcal/mol
Surface area15500 Å2
MethodPISA
2
A: NADPH-dependent FMN reductase
B: NADPH-dependent FMN reductase
hetero molecules

A: NADPH-dependent FMN reductase
B: NADPH-dependent FMN reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,25710
Polymers86,5954
Non-polymers2,6626
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area12680 Å2
ΔGint-52 kcal/mol
Surface area26600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.030, 89.140, 71.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 2 - 183 / Label seq-ID: 2 - 183

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsDIMER-TETRAMER EQUILIBRIUM

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Components

#1: Protein NADPH-dependent FMN reductase


Mass: 21648.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: PD1222 / Gene: ferB, Pden_4071 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: A1B9E3
#2: Chemical ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23N4O9P
#3: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 15% PEG 4000, 0.2M Ammonium sulphate, 0.1M Sodium acetate, 0.1M MES buffer pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.97522, 0.97714, 0.97753
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 5, 2009
RadiationMonochromator: Double crystal Si(111), horizontally focussing
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.975221
20.977141
30.977531
ReflectionResolution: 1.4→19.56 Å / Num. obs: 75170 / % possible obs: 76.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 1.4→1.436 Å / % possible all: 86.04

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Processing

Software
NameVersionClassification
MAR345v.0.10.22data collection
Auto-Rickshawphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.4→19.11 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.598 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17386 3037 4 %RANDOM
Rwork0.16009 ---
obs0.16065 72133 97.36 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.834 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å20 Å2
2---0.14 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2848 0 90 451 3389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193071
X-RAY DIFFRACTIONr_bond_other_d0.0050.022969
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9964165
X-RAY DIFFRACTIONr_angle_other_deg2.38636859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.1865364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9423.926135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67615491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8181518
X-RAY DIFFRACTIONr_chiral_restr0.0940.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0213362
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02684
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2981.51799
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.08422892
X-RAY DIFFRACTIONr_scbond_it3.64831233
X-RAY DIFFRACTIONr_scangle_it5.244.51221
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11446 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 217 -
Rwork0.214 4622 -
obs--86.06 %
Refinement TLS params.

T22: 0.0277 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1327-0.0319-0.03510.32050.12930.4528-0.00830.023-0.0144-0.01490.01040.03490.0485-0.0266-0.0020.0097-0.0109-0.00380.0020.017818.073-12.61346.026
20.08010.002-0.01180.37960.13060.4502-0.0041-0.01440.00780.02390.01090.0335-0.0362-0.0277-0.00690.0090.01190.00560.00260.016517.36911.74360.872
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 182
2X-RAY DIFFRACTION2B2 - 182

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