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- PDB-5thx: Crystal Structure of a ferredoxin NADP+ reductase from Neisseria ... -

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Basic information

Entry
Database: PDB / ID: 5thx
TitleCrystal Structure of a ferredoxin NADP+ reductase from Neisseria gonorrhoeae with bound NADP and FAD
ComponentsFerredoxin--NADP reductase
KeywordsOXIDOREDUCTASE / SSGCID / Neisseria gonorrhoeae / ferredoxin NADP+ reductase / NADP / FAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


ferredoxin-NADP+ reductase activity / 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 / Flavoprotein pyridine nucleotide cytochrome reductase / 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 / 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 speciesNeisseria gonorrhoeae MIA_2011_03-10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a ferredoxin NADP+ reductase from Neisseria gonorrhoeae with bound NADP and FAD
Authors: Phan, J.N. / Dranow, D.M. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionSep 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferredoxin--NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0004
Polymers30,4471
Non-polymers1,5533
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-18 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.010, 60.010, 158.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ferredoxin--NADP reductase


Mass: 30446.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae MIA_2011_03-10 (bacteria)
Gene: M736_00365 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3GW31
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus (274695 A1): 10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.3 M MgCl2, 0.3 M CaCl, 0.1 M MES/Imidazole pH 6.5 Direct cryo; Protein Concentration: 20.5 mg/mL; puck id: ifb3-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 4, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 43054 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.53 % / Biso Wilson estimate: 17.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 21.5
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.55-1.590.4973.990.951100
1.59-1.630.3815.230.9681100
1.63-1.680.3226.160.9771100
1.68-1.730.2477.910.9831100
1.73-1.790.1999.770.991100
1.79-1.850.16212.190.9921100
1.85-1.920.12115.590.9971100
1.92-20.09818.970.9971100
2-2.090.08322.790.9981100
2.09-2.190.07325.580.9981100
2.19-2.310.06429.150.9981100
2.31-2.450.05931.690.9981100
2.45-2.620.05633.640.9991100
2.62-2.830.05136.90.998199.9
2.83-3.10.04640.790.9991100
3.1-3.470.04343.130.9991100
3.47-40.04145.180.9991100
4-4.90.03946.340.9991100
4.9-6.930.03844.380.9991100
6.93-500.03840.950.998197.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3crz

3crz


Resolution: 1.55→37.396 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.3
RfactorNum. reflection% reflection
Rfree0.1882 1988 4.63 %
Rwork0.1587 --
obs0.16 42944 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.72 Å2 / Biso mean: 24.0886 Å2 / Biso min: 10.77 Å2
Refinement stepCycle: final / Resolution: 1.55→37.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 155 364 2561
Biso mean--18.22 34.98 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052318
X-RAY DIFFRACTIONf_angle_d0.9093182
X-RAY DIFFRACTIONf_chiral_restr0.055348
X-RAY DIFFRACTIONf_plane_restr0.005482
X-RAY DIFFRACTIONf_dihedral_angle_d15.0251436
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.55-1.58880.22631300.196928713001
1.5888-1.63170.24671420.179728833025
1.6317-1.67980.20441440.181928482992
1.6798-1.7340.20331400.168428643004
1.734-1.79590.23961240.174828953019
1.7959-1.86780.22021460.17128873033
1.8678-1.95290.1971380.16328953033
1.9529-2.05580.18661250.159729173042
2.0558-2.18460.20521400.162829013041
2.1846-2.35320.18161450.159729323077
2.3532-2.590.18591400.16629343074
2.59-2.96470.18131620.164629533115
2.9647-3.73460.1781480.152330083156
3.7346-37.40730.17351640.14231683332
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)
12.61850.13030.58621.60350.24021.26190.10950.1304-0.2843-0.09840.09240.45680.282-0.3093-0.17990.1677-0.0678-0.02180.22270.01420.232915.212-4.25279.26
22.6130.0553-0.29972.288-0.68711.4720.0218-0.0146-0.2180.00340.1250.42530.3028-0.5492-0.06410.1356-0.0694-0.00640.26140.03180.213913.582-1.71711.7669
32.4184-0.4350.74142.0253-0.03120.61280.0898-0.2444-0.42510.12910.16440.40620.4301-0.4697-0.22030.2364-0.08320.02950.23590.09070.307513.1407-8.493720.0075
44.5245.2534-0.91726.9035-2.08582.0627-0.06190.17450.3421-0.10420.10060.4426-0.0241-0.19330.00750.09830.0275-0.01180.18060.01920.157719.56915.365.6822
51.9140.49180.5712.6713-0.37873.5703-0.02280.17720.0812-0.1227-0.05060.0192-0.04150.02020.07040.07290.0129-0.0020.13720.00830.113429.51248.93386.4458
61.9042-0.42742.6240.9297-1.20438.75060.1970.2039-0.1321-0.12-0.07440.01980.76470.2492-0.13780.17230.0113-0.00590.14730.00010.151433.2371-3.0278.3434
72.77780.43694.37631.75970.84167.1340.06260.4027-0.0805-0.15120.0524-0.18850.18940.5509-0.10680.10860.01250.02550.19080.00830.165536.90495.12424.3623
80.9301-0.70831.15360.9924-0.82611.9902-0.13860.13830.22180.0914-0.1194-0.2782-0.12360.21270.26150.113-0.0147-0.03780.16240.03880.208538.676313.041315.5132
92.53660.13180.563.7499-0.78642.2647-0.1097-0.16570.06610.22390.01120.0417-0.09260.00750.09180.11380.0334-0.0040.1495-0.02450.107424.474518.418317.2474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 36 )A2 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 69 )A37 - 69
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 92 )A70 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 108 )A93 - 108
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 144 )A109 - 144
6X-RAY DIFFRACTION6chain 'A' and (resid 145 through 166 )A145 - 166
7X-RAY DIFFRACTION7chain 'A' and (resid 167 through 180 )A167 - 180
8X-RAY DIFFRACTION8chain 'A' and (resid 181 through 221 )A181 - 221
9X-RAY DIFFRACTION9chain 'A' and (resid 222 through 258 )A222 - 258

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