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- PDB-2b5o: ferredoxin-NADP reductase -

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Basic information

Entry
Database: PDB / ID: 2b5o
Titleferredoxin-NADP reductase
ComponentsFerredoxin--NADP reductase
KeywordsOXIDOREDUCTASE / complex with FAD
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / phycobilisome
Similarity search - Function
Ferredoxin--NADP reductase, plant and Cyanobacteria type / CpcD-like domain / Ferredoxin--NADP reductase / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase ...Ferredoxin--NADP reductase, plant and Cyanobacteria type / CpcD-like domain / Ferredoxin--NADP reductase / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7002 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.499 Å
AuthorsSawaya, M.R. / Kerfeld, C.A. / Gomez-Lojero, C. / Krogmann, D. / Bryant, D.A. / Yeates, T.O.
CitationJournal: To be Published
Title: Crystal Structure of Ferredoxin-NADP reductase from Synechococcus sp. (PCC 7002)
Authors: Sawaya, M.R. / Kerfeld, C.A. / Gomez-Lojero, C. / Krogmann, D. / Bryant, D.A. / Yeates, T.O.
History
DepositionSep 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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

Downloads & links

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Assembly

Deposited unit
A: Ferredoxin--NADP reductase
B: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,76715
Polymers90,1402
Non-polymers2,62813
Water1,65792
1
A: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3367
Polymers45,0701
Non-polymers1,2666
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4328
Polymers45,0701
Non-polymers1,3627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.985, 121.985, 74.729
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPRO1AA111 - 167111 - 167
21SERSERPROPRO1BB111 - 167111 - 167
32GLYGLYHISHIS1AA168 - 176168 - 176
42GLYGLYHISHIS1BB168 - 176168 - 176
53LYSLYSLEULEU1AA177 - 204177 - 204
63LYSLYSLEULEU1BB177 - 204177 - 204
74TYRTYRPROPRO1AA206 - 312206 - 312
84TYRTYRPROPRO1BB206 - 312206 - 312
95ASNASNGLNGLN1AA314 - 325314 - 325
105ASNASNGLNGLN1BB314 - 325314 - 325
116THRTHRGLUGLU3AA327 - 378327 - 378
126THRTHRGLUGLU3BB327 - 378327 - 378
137LYSLYSASNASN6AA379 - 383379 - 383
147LYSLYSASNASN6BB379 - 383379 - 383
158GLUGLUTYRTYR1AA385 - 402385 - 402
168GLUGLUTYRTYR1BB385 - 402385 - 402
DetailsThe biological assembly is a monomer. The asymmetric unit contains two monomers.

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Components

#1: Protein Ferredoxin--NADP reductase / FNR


Mass: 45069.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: P31973, ferredoxin-NADP+ reductase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 1.78 Å3/Da / Density % sol: 30.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2M ammonium sulfate, 5% isopropanol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2003 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→90 Å / Num. all: 22511 / Num. obs: 22511 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.095 / Χ2: 1.118 / Net I/σ(I): 22.5
Reflection shellResolution: 2.5→2.59 Å / % possible obs: 100 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 4.08 / Num. measured obs: 2219 / Num. unique all: 2219 / Χ2: 0.956 / % possible all: 100

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Phasing

Phasing MRRfactor: 0.535 / Cor.coef. Fo:Fc: 0.293
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.7data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1b2r

1b2r


Resolution: 2.499→47.14 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.172 / SU B: 18.657 / SU ML: 0.2 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.31 / Stereochemistry target values: Engh & Huber
Details: N-terminal 110 residues are either disordered or proteolyzed. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 2149 9.901 %random
Rwork0.1785 ---
all0.184 21704 --
obs0.184 21704 96.501 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.853 Å2
Baniso -1Baniso -2Baniso -3
1-0.277 Å20.139 Å20 Å2
2--0.277 Å20 Å2
3----0.416 Å2
Refinement stepCycle: LAST / Resolution: 2.499→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4680 0 161 92 4933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224952
X-RAY DIFFRACTIONr_bond_other_d0.0010.024290
X-RAY DIFFRACTIONr_angle_refined_deg1.9142.0026724
X-RAY DIFFRACTIONr_angle_other_deg0.968310040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8375582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46424.224232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.91215840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3751530
X-RAY DIFFRACTIONr_chiral_restr0.0950.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025384
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02968
X-RAY DIFFRACTIONr_nbd_refined0.2140.31012
X-RAY DIFFRACTIONr_nbd_other0.2140.34326
X-RAY DIFFRACTIONr_nbtor_refined0.1950.52376
X-RAY DIFFRACTIONr_nbtor_other0.0970.52737
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.5348
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0670.54
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.335
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.362
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.515
X-RAY DIFFRACTIONr_mcbond_it4.18423744
X-RAY DIFFRACTIONr_mcbond_other0.96721188
X-RAY DIFFRACTIONr_mcangle_it4.67234700
X-RAY DIFFRACTIONr_mcangle_other3.233964
X-RAY DIFFRACTIONr_scbond_it5.94922510
X-RAY DIFFRACTIONr_scbond_other2.36723879
X-RAY DIFFRACTIONr_scangle_it7.54332024
X-RAY DIFFRACTIONr_scangle_other3.936076
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberRmsTypeWeight
38520.055TIGHT POSITIONAL0.05
5390.308LOOSE POSITIONAL5
38520.256TIGHT THERMAL0.5
5394.281LOOSE THERMAL10
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.499-2.5640.3021510.2061301160190.693
2.564-2.6340.2811400.1921327160691.345
2.634-2.710.2511620.1941292157392.435
2.71-2.7930.3071400.2131262148694.347
2.793-2.8840.2871350.1941247146394.463
2.884-2.9850.2451370.171257145296.006
2.985-3.0970.2641170.1921199135697.05
3.097-3.2230.2311290.1841167132198.107
3.223-3.3660.2741160.1961123125898.49
3.366-3.5290.2211290.1761077122498.529
3.529-3.7190.2181100.1721048116799.229
3.719-3.9430.2431120.176998111799.373
3.943-4.2130.2960.163928103698.842
4.213-4.5480.1861050.14485296599.171
4.548-4.9770.217800.15281189899.22
4.977-5.5570.228780.18573281499.509
5.557-6.4020.265820.19864773499.319
6.402-7.8050.201590.1854560699.67
7.805-10.8890.185450.15346050699.802
10.889-47.140.233260.22282308100
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)
11.519-0.32070.44810.18210.1130.50890.07890.00240.2869-0.0358-0.08110.1019-0.0569-0.05480.0022-0.0629-0.02830.0259-0.0933-0.0098-0.01121.715349.9312-4.3384
22.01181.15740.18961.97610.28380.91050.3814-0.4807-0.18780.5685-0.26790.01880.0727-0.0814-0.11350.1422-0.1008-0.0350.0330.0635-0.0381-28.721322.843311.8197
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A111 - 402
2X-RAY DIFFRACTION2B111 - 402

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