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- PDB-2rc6: Refined structure of FNR from Leptospira interrogans bound to NADP+ -

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Basic information

Entry
Database: PDB / ID: 2rc6
TitleRefined structure of FNR from Leptospira interrogans bound to NADP+
ComponentsFerredoxin-NADP reductase
KeywordsOXIDOREDUCTASE / FNR
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
Ferredoxin--NADP reductase / 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. ...Ferredoxin--NADP reductase / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesLeptospira interrogans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsNascimento, A.S. / Catalano-Dupuy, D.L. / Ceccarelli, E.A. / Polikarpov, I.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: Crystal structures of Leptospira interrogans FAD-containing ferredoxin-NADP+ reductase and its complex with NADP+.
Authors: Nascimento, A.S. / Catalano-Dupuy, D.L. / Bernardes, A. / Neto, M.O. / Santos, M.A. / Ceccarelli, E.A. / Polikarpov, I.
History
DepositionSep 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Feb 21, 2024Group: 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 / 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.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_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
C: Ferredoxin-NADP reductase
D: Ferredoxin-NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,81821
Polymers139,8684
Non-polymers6,95017
Water4,324240
1
A: Ferredoxin-NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7546
Polymers34,9671
Non-polymers1,7865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Ferredoxin-NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6885
Polymers34,9671
Non-polymers1,7214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Ferredoxin-NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6885
Polymers34,9671
Non-polymers1,7214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: Ferredoxin-NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6885
Polymers34,9671
Non-polymers1,7214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.168, 112.251, 92.399
Angle α, β, γ (deg.)90.00, 93.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTYRTYRchain A and (resseq 7:122 or resseq 125:314 or resseq 415:416 )AA7 - 1227 - 122
12ASNASNTYRTYRchain A and (resseq 7:122 or resseq 125:314 or resseq 415:416 )AA125 - 314125 - 314
13FADFADNAPNAPchain A and (resseq 7:122 or resseq 125:314 or resseq 415:416 )AH - I415 - 416
21PROPROTYRTYRchain B and (resseq 7:122 or resseq 125:314 or resseq 415:416 )BB7 - 1227 - 122
22ASNASNTYRTYRchain B and (resseq 7:122 or resseq 125:314 or resseq 415:416 )BB125 - 314125 - 314
23FADFADNAPNAPchain B and (resseq 7:122 or resseq 125:314 or resseq 415:416 )BL - M415 - 416
31PROPROTYRTYRchain C and (resseq 7:122 or resseq 125:314 or resseq 415:416 )CC7 - 1227 - 122
32ASNASNTYRTYRchain C and (resseq 7:122 or resseq 125:314 or resseq 415:416 )CC125 - 314125 - 314
33FADFADNAPNAPchain C and (resseq 7:122 or resseq 125:314 or resseq 415:416 )CP - Q415 - 416
41PROPROTYRTYRchain D and (resseq 7:122 or resseq 125:314 or resseq 415:416 )DD7 - 1227 - 122
42ASNASNTYRTYRchain D and (resseq 7:122 or resseq 125:314 or resseq 415:416 )DD125 - 314125 - 314
43FADFADNAPNAPchain D and (resseq 7:122 or resseq 125:314 or resseq 415:416 )DT - U415 - 416

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Ferredoxin-NADP reductase


Mass: 34967.098 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans (bacteria) / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EY89, ferredoxin-NADP+ reductase

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Non-polymers , 5 types, 257 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#6: Water ChemComp-HOH / 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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 27% PEG3350, 0.3M ammonium fluoride, 50mM Tris-HCL buffer, pH 7.0, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2005 / Details: mirrors
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.61→92.45 Å / Num. obs: 36768 / % possible obs: 87.8 % / Redundancy: 3 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.61-2.752.50.73410.734167.4
2.75-2.922.40.4721.60.472176.9
2.92-3.122.50.2942.50.294183.8
3.12-3.372.60.1754.20.175189.2
3.37-3.692.80.126.10.12194.1
3.69-4.133.10.0927.70.092198.7
4.13-4.773.60.0749.30.0741100
4.77-5.843.90.0798.80.0791100
5.84-8.2540.0710.30.071100
8.25-112.513.80.04511.60.045199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→33.532 Å / SU ML: 0.45 / Phase error: 27.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2759 1723 4.97 %
Rwork0.2346 --
obs0.2367 34641 92.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 18.878 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 28.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.819 Å2-0 Å20.109 Å2
2---1.924 Å20 Å2
3---1.105 Å2
Refinement stepCycle: LAST / Resolution: 2.7→33.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9496 0 445 240 10181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310171
X-RAY DIFFRACTIONf_angle_d0.77113781
X-RAY DIFFRACTIONf_dihedral_angle_d17.7033912
X-RAY DIFFRACTIONf_chiral_restr0.0541432
X-RAY DIFFRACTIONf_plane_restr0.0041712
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2475X-RAY DIFFRACTIONPOSITIONAL0.012
12B2475X-RAY DIFFRACTIONPOSITIONAL0.012
13C2475X-RAY DIFFRACTIONPOSITIONAL0.009
14D2475X-RAY DIFFRACTIONPOSITIONAL0.011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.7790.3681030.2882314241777
2.779-2.8690.3471390.2892371251081
2.869-2.9720.3151380.2762509264785
2.972-3.0910.3261340.272584271887
3.091-3.2310.331310.2612655278690
3.231-3.4010.3021390.2492720285992
3.401-3.6140.2621440.2332828297295
3.614-3.8930.2511790.2062906308599
3.893-4.2840.2371400.19129983138100
4.284-4.9020.191560.16929923148100
4.902-6.170.2421490.1930123161100
6.17-33.5340.2271710.20330293200100
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)
10.25680.4649-0.04990.0835-0.17840.3843-0.0588-0.02630.12190.0511-0.0031-0.01270.0468-0.03930.05580.13710.0404-0.01120.0986-0.03340.12952.437917.18072.5038
20.3325-0.19330.10310.4196-0.50810.5078-0.0441-0.0228-0.0765-0.02170.0902-0.017-0.0344-0.0703-0.02290.1570.01130.0260.1091-0.00780.1123-30.6166-7.3061-0.2435
30.36060.21670.47760.602-0.06430.8377-0.1318-0.08320.00580.0461-0.0608-0.0326-0.0569-0.0720.11910.10010.03010.02910.12580.00170.11220.0522-0.6699-43.7223
40.5876-0.12530.15530.33110.18930.4518-0.0417-0.00460.0897-0.03180.0167-0.0701-0.0194-0.02690.01340.12140.0348-0.02070.138-0.0130.2352-33.833124.0611-46.1172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA7 - 314
2X-RAY DIFFRACTION2chain BB7 - 314
3X-RAY DIFFRACTION3chain CC7 - 314
4X-RAY DIFFRACTION4chain DD7 - 314

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