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- PDB-4fk8: Crystal structure of FERREDOXIN-NADP REDUCTASE from burkholderia ... -

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Basic information

Entry
Database: PDB / ID: 4fk8
TitleCrystal structure of FERREDOXIN-NADP REDUCTASE from burkholderia thailandensis E264 with bound FAD
ComponentsFerredoxin--NADP reductase
KeywordsOXIDOREDUCTASE / SSGCID / NIH / NIAID / Structural Genomics / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / heme catabolic process / cellular response to oxidative stress / nucleotide binding
Similarity search - Function
: / Ferredoxin--NADP reductase, bacteria / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type ...: / Ferredoxin--NADP reductase, bacteria / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / 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 speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionJun 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)62,4914
Polymers60,9202
Non-polymers1,5712
Water3,657203
1
A: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2452
Polymers30,4601
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2452
Polymers30,4601
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.580, 86.200, 102.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ferredoxin--NADP reductase


Mass: 30459.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_I0211 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2T230, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7
Details: EBS INTERNAL TRACKING NUMBER 229491d3 HEPES (PH 7.0), 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH 20% PEG 3350, 200 MM NACL. SOAKED FOR 5 DAYS WITH 1 ...Details: EBS INTERNAL TRACKING NUMBER 229491d3 HEPES (PH 7.0), 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH 20% PEG 3350, 200 MM NACL. SOAKED FOR 5 DAYS WITH 1 MM FAD. 20% ETHYLENE GLYCOL used as CRYOPROTECTANT, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 36808 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.33 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.59
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 4.3 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→43.94 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.819 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1839 5 %RANDOM
Rwork0.198 ---
obs0.199 36808 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.5 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3775 0 106 203 4084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023998
X-RAY DIFFRACTIONr_angle_refined_deg1.4042.015473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7055495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52723.377151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83615614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8361519
X-RAY DIFFRACTIONr_chiral_restr0.0920.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212971
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 116 -
Rwork0.232 2222 -
obs--92.27 %
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)
10.21830.2586-0.3111.18750.51721.35130.0582-0.0209-0.00370.1453-0.05820.0220.0471-0.0105-0.00010.2095-0.0036-0.00290.1417-0.00880.1733-9.773-9.887929.4657
20.5505-0.05150.11260.75530.04861.80580.0081-0.0150.01560.07020.01520.02190.1374-0.1803-0.02330.1791-0.0090.00790.161-0.01810.1629-15.5841-9.787927.6664
32.15710.54250.160.1836-0.2011.3197-0.15220.276-0.0249-0.02790.0855-0.02390.02160.03540.06670.2145-0.0126-0.0030.2011-0.01440.1297-8.7788-4.44967.808
40.16250.5154-0.1792.88540.5161.6061-0.01190.02190.03640.15420.0696-0.01-0.15340.1939-0.05780.1877-0.0613-0.04920.17970.01790.1581-3.72582.079919.0544
51.43190.31321.59461.3319-0.76592.8027-0.67680.30690.089-0.17440.4595-0.0516-0.75970.10660.21740.3572-0.1306-0.03570.32150.04090.021-6.76387.05497.6656
62.19340.2414-0.20810.9481-0.26082.9753-0.23430.25990.0435-0.05440.23560.1752-0.0605-0.2322-0.00120.1491-0.032-0.08180.23430.04410.1106-19.7873-0.72784.0497
73.98743.8292.36644.34010.67375.42030.27240.02470.29070.5501-0.05580.4659-0.41350.0431-0.21660.2872-0.03750.09420.1156-0.05220.15881.12216.853444.2181
81.14490.4595-0.07521.0833-0.05820.14620.0429-0.0683-0.00490.1398-0.09740.064-0.07340.02460.05450.196-0.03740.01290.150.00980.18014.35848.27939.6845
90.76880.73290.13531.12550.06750.1830.1738-0.0635-0.02630.1454-0.08690.0568-0.03780.0293-0.08690.196-0.0390.00890.16180.0140.1653.54035.503642.34
100.6364-0.0314-0.08710.7966-0.13970.44230.09850.013-0.08090.0967-0.1054-0.13180.01460.14320.00690.1330.0014-0.02080.17360.00010.220817.3012.926633.0363
112.44-0.37030.981.4219-0.72540.7940.04960.2335-0.3875-0.15370.0896-0.10880.0528-0.0298-0.13920.13510.0369-0.00680.1407-0.0530.224418.2868-4.443426.6418
122.93360.3106-0.57453.18920.65380.42750.2483-0.0653-0.22290.4194-0.0428-0.6341-0.07370.0486-0.20560.1851-0.0459-0.1090.1720.0580.366429.0302-0.344439.8441
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 46
2X-RAY DIFFRACTION2A47 - 113
3X-RAY DIFFRACTION3A114 - 152
4X-RAY DIFFRACTION4A153 - 178
5X-RAY DIFFRACTION5A179 - 220
6X-RAY DIFFRACTION6A221 - 271
7X-RAY DIFFRACTION7B17 - 24
8X-RAY DIFFRACTION8B25 - 61
9X-RAY DIFFRACTION9B62 - 100
10X-RAY DIFFRACTION10B101 - 167
11X-RAY DIFFRACTION11B168 - 220
12X-RAY DIFFRACTION12B221 - 271

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