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- PDB-4f7d: Crystal structure of ferredoxin-NADP reductase from burkholderia ... -

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Basic information

Entry
Database: PDB / ID: 4f7d
TitleCrystal structure of ferredoxin-NADP reductase from burkholderia thailandensis E264
ComponentsFerredoxin--NADP reductase
KeywordsOXIDOREDUCTASE / SSGCID / NIH / NIAID / SBRI / UW / EMERALD BIOSTRUCTURES / FERREDOXIN-NADP REDUCTASE / 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
ferredoxin--NADP(+) reductase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 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
DepositionMay 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)60,9202
Polymers60,9202
Non-polymers00
Water2,504139
1
A: Ferredoxin--NADP reductase


Theoretical massNumber of molelcules
Total (without water)30,4601
Polymers30,4601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferredoxin--NADP reductase


Theoretical massNumber of molelcules
Total (without water)30,4601
Polymers30,4601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.020, 85.570, 102.140
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: EBS INTERNAL TRACKING NUMBER 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, 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: May 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.35→102.14 Å / Num. obs: 26192 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.39 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 20.49
Reflection shellResolution: 2.35→2.41 Å / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 4.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→102.14 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / SU B: 13.702 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.318 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1329 5.1 %RANDOM
Rwork0.204 ---
obs0.206 26143 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.46 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å20 Å20 Å2
2--1.63 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.35→102.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 0 139 3901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023865
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.9765276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5445493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.78323.766154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20615598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.341517
X-RAY DIFFRACTIONr_chiral_restr0.0880.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212913
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 80 -
Rwork0.27 1673 -
obs--99.72 %
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)
160.608516.360931.477219.4863-5.331336.446-0.57910.71693.096-0.6229-0.22091.0528-0.0518-0.11170.79990.31260.0302-0.04470.1290.07650.286929.375519.28033.3565
21.63580.01580.59722.3225-0.20121.05470.03150.2070.1145-0.3159-0.0776-0.104-0.05020.05160.0460.0910.02660.02050.07650.01430.050330.93158.807910.3149
32.06-1.56120.21522.8528-0.79022.32280.0550.0867-0.1515-0.2030.00740.10690.071-0.0835-0.06230.0637-0.0098-0.02790.05440.00430.098427.76145.554711.4692
41.7519-0.17480.00141.4990.00631.38630.0882-0.0935-0.1593-0.0191-0.02470.28720.0192-0.2355-0.06350.0157-0.0065-0.02160.06080.01430.100520.56552.230919.6477
55.6791-1.69451.67228.5484-3.28466.97370.0028-0.3041-0.69120.06410.27750.75420.8325-0.8493-0.28030.2143-0.2189-0.07320.3140.06370.44395.4303-9.804119.2671
65.4393-0.3096-0.28933.3932-0.07114.80890.00610.4708-0.1324-0.11660.26750.54050.1104-0.852-0.27360.0423-0.0337-0.10650.32110.04910.3074.91730.391910.2023
71.5508-0.80990.4091.7566-0.3351.17260.0730.1352-0.0672-0.105-0.0598-0.15450.12460.1398-0.01320.0842-0.01260.00850.0651-0.00670.082348.3358-11.225222.2516
81.1209-0.60420.11821.992-0.8093.4169-0.03320.20040.1262-0.0824-0.0253-0.1404-0.09910.21860.05850.0395-0.0184-0.01390.06280.01560.093848.6533-8.445722.9652
93.6116-0.65540.54180.95140.9021.2997-0.3367-0.54620.09040.18030.13920.10190.063-0.06880.19760.18570.0514-0.05760.1315-0.04540.081744.0853-3.084142.2486
101.7336-0.52090.73372.4172-0.30792.6065-0.1931-0.16560.21890.18030.1943-0.0047-0.2684-0.269-0.00120.13810.0642-0.03240.1096-0.06130.103438.88443.101736.3691
114.5974-0.8104-1.24764.51560.86454.6991-0.3268-0.93940.38720.45380.3008-0.0788-0.12630.43910.0260.20540.0751-0.14640.2912-0.1150.143652.90041.74548.858
127.57990.32492.2488.612-4.585429.6494-1.07560.1877-0.0476-2.3561-0.9543-0.6910.57592.61172.030.83090.17430.13470.43660.04470.377757.1759-2.874832.6198
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 20
2X-RAY DIFFRACTION2A21 - 64
3X-RAY DIFFRACTION3A65 - 90
4X-RAY DIFFRACTION4A91 - 193
5X-RAY DIFFRACTION5A194 - 231
6X-RAY DIFFRACTION6A232 - 267
7X-RAY DIFFRACTION7B18 - 66
8X-RAY DIFFRACTION8B67 - 114
9X-RAY DIFFRACTION9B115 - 159
10X-RAY DIFFRACTION10B160 - 213
11X-RAY DIFFRACTION11B214 - 264
12X-RAY DIFFRACTION12B265 - 271

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