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- PDB-3lzx: Crystal structure of ferredoxin-NADP+ oxidoreductase from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 3lzx
TitleCrystal structure of ferredoxin-NADP+ oxidoreductase from Bacillus subtilis (FORM II)
ComponentsFerredoxin--NADP reductase 2
KeywordsOXIDOREDUCTASE / ferredoxin reductase / FAD / NADPH / Flavoprotein / NADP
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / thioredoxin-disulfide reductase (NADPH) activity / cell redox homeostasis / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
Ferredoxin--NADP reductase, type 2 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ferredoxin--NADP reductase 2
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKomori, H. / Seo, D. / Sakurai, T. / Higuchi, Y.
CitationJournal: Protein Sci. / Year: 2010
Title: Crystal structure analysis of Bacillus subtilis ferredoxin-NADP(+) oxidoreductase and the structural basis for its substrate selectivity
Authors: Komori, H. / Seo, D. / Sakurai, T. / Higuchi, Y.
History
DepositionMar 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Ferredoxin--NADP reductase 2
B: Ferredoxin--NADP reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8748
Polymers73,7702
Non-polymers3,1046
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-25 kcal/mol
Surface area29760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.466, 64.850, 61.116
Angle α, β, γ (deg.)90.00, 105.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ferredoxin--NADP reductase 2 / ferredoxin-NADP+ oxidoreductase / Fd-NADP+ reductase 2 / FNR 2


Mass: 36884.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pETBlue-1 / Production host: Escherichia coli (E. coli) / References: UniProt: O05268, ferredoxin-NADP+ reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 3350, 0.2M Sodium fluoride, 5% Trehalose, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 18, 2008
RadiationMonochromator: Fixed exit Si 111 double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→26.85 Å / Num. obs: 59771 / % possible obs: 96.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.051
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.22 / % possible all: 80.4

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LZW

3lzw


Resolution: 1.9→26.85 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.303 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 3014 5 %RANDOM
Rwork0.18113 ---
obs0.18267 56728 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.974 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å2-0.99 Å2
2---0.31 Å20 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.9→26.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5140 0 204 516 5860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225456
X-RAY DIFFRACTIONr_bond_other_d0.0010.023628
X-RAY DIFFRACTIONr_angle_refined_deg1.3252.0167412
X-RAY DIFFRACTIONr_angle_other_deg0.813.0048794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6085656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3825.25240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67315936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4361522
X-RAY DIFFRACTIONr_chiral_restr0.1290.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021016
X-RAY DIFFRACTIONr_nbd_refined0.1890.2962
X-RAY DIFFRACTIONr_nbd_other0.1820.23894
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22574
X-RAY DIFFRACTIONr_nbtor_other0.0810.22796
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2470
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1440.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0670.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5131.53258
X-RAY DIFFRACTIONr_mcbond_other0.1071.51344
X-RAY DIFFRACTIONr_mcangle_it0.96525246
X-RAY DIFFRACTIONr_scbond_it1.50532270
X-RAY DIFFRACTIONr_scangle_it2.4234.52166
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 190 -
Rwork0.214 3320 -
obs--100 %
Refinement TLS params.

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)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.90720.27710.10680.5030.1120.229-0.01830.03220.0007-0.00950.0277-0.01030.01670.0244-0.0093-0.0102-0.00720.0071-0.0275-0.0034-0.032735.9546-11.55725.5707
21.81870.54810.75231.59920.31221.69340.0777-0.1215-0.06810.0718-0.0834-0.04860.1724-0.13320.0057-0.0156-0.0494-0.01780.0041-0.0132-0.103650.4851-5.741356.6331
31.05530.19270.19730.556-0.08750.308-0.06380.04050.2523-0.02470.00730.19130.0144-0.03330.0564-0.0477-0.0037-0.0328-0.04480.02980.083910.9926-1.288720.4274
41.73-0.14280.7270.7302-0.15571.4261-0.07660.1118-0.04990.02190.05320.0082-0.06130.05790.0234-0.0365-0.0269-0.0206-0.0028-0.0272-0.0563-11.9769-25.848214.417
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 125
2X-RAY DIFFRACTION1A250 - 329
3X-RAY DIFFRACTION2A126 - 249
4X-RAY DIFFRACTION3B1 - 125
5X-RAY DIFFRACTION3B250 - 329
6X-RAY DIFFRACTION4B126 - 249

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