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- PDB-3lzw: Crystal structure of ferredoxin-NADP+ oxidoreductase from bacillu... -

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Basic information

Entry
Database: PDB / ID: 3lzw
TitleCrystal structure of ferredoxin-NADP+ oxidoreductase from bacillus subtilis (form I)
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 / flavin adenine dinucleotide binding / NADP 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: 1.8 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_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.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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4605
Polymers36,8851
Non-polymers1,5754
Water4,324240
1
A: Ferredoxin--NADP reductase 2
hetero molecules

A: Ferredoxin--NADP reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,92010
Polymers73,7702
Non-polymers3,1508
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3420 Å2
ΔGint-27 kcal/mol
Surface area29700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.900, 135.724, 39.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-526-

HOH

21A-528-

HOH

31A-566-

HOH

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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.: 1
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 / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES buffer (pH 7.5), 30% 1,2-propanediol, 20% PEG 400, 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: 1.8→26.87 Å / Num. obs: 32363 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.071
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.388 / % possible all: 99.5

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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 2ZBW

2zbw


Resolution: 1.8→26.87 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.875 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19645 1602 5 %RANDOM
Rwork0.16885 ---
obs0.17023 30707 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: 24.212 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.71 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.8→26.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 103 240 2913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222728
X-RAY DIFFRACTIONr_bond_other_d0.0010.021814
X-RAY DIFFRACTIONr_angle_refined_deg1.2532.0163706
X-RAY DIFFRACTIONr_angle_other_deg0.7993.0044397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.35328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80725.25120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41715468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.9771511
X-RAY DIFFRACTIONr_chiral_restr0.1330.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022975
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02508
X-RAY DIFFRACTIONr_nbd_refined0.1950.2457
X-RAY DIFFRACTIONr_nbd_other0.1760.21903
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21284
X-RAY DIFFRACTIONr_nbtor_other0.0810.21378
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2199
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1070.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1170.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4221.51629
X-RAY DIFFRACTIONr_mcbond_other0.0911.5672
X-RAY DIFFRACTIONr_mcangle_it0.79622623
X-RAY DIFFRACTIONr_scbond_it1.23731136
X-RAY DIFFRACTIONr_scangle_it1.9764.51083
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 102 -
Rwork0.206 2203 -
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)
10.80690.21890.29460.6072-0.00470.7368-0.00610.00610.02770.02410.0170.05420.028-0.0858-0.0109-0.0389-0.00790.008-0.02780.0071-0.03-12.6999-5.356210.7321
23.9590.8593-0.64184.2882-1.67023.2639-0.2346-0.0545-0.2018-0.5710.15810.04970.8102-0.12770.07640.1375-0.0633-0.0036-0.16330.0442-0.0898-14.4038-34.592828.3066
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 125
2X-RAY DIFFRACTION1A250 - 329
3X-RAY DIFFRACTION2A126 - 249

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