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

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Basic information

Entry
Database: PDB / ID: 5ufa
TitleCrystal Structure of a ferredoxin NADP+ reductase from Neisseria gonorrhoeae with bound FAD and NADP
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / SSGCID / Neisseria gonorrhoeae / ferredoxin NADP+ reductase / FAD / NADP / 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 / 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 ...Ferredoxin--NADP reductase, bacteria / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Putative oxidoreductase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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 FAD and NADP
Authors: Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJan 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Oxidoreductase
B: Oxidoreductase
C: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4299
Polymers90,8423
Non-polymers4,5876
Water3,459192
1
A: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8103
Polymers30,2811
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8103
Polymers30,2811
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8103
Polymers30,2811
Non-polymers1,5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.190, 164.190, 167.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 33 or (resid 34...
21(chain B and (resid 6 through 33 or (resid 34...
31(chain C and (resid 6 through 33 or (resid 34...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 6 through 33 or (resid 34...A6 - 33
121(chain A and (resid 6 through 33 or (resid 34...A34
131(chain A and (resid 6 through 33 or (resid 34...A6 - 259
141(chain A and (resid 6 through 33 or (resid 34...A6 - 259
151(chain A and (resid 6 through 33 or (resid 34...A6 - 259
161(chain A and (resid 6 through 33 or (resid 34...A6 - 259
211(chain B and (resid 6 through 33 or (resid 34...B6 - 33
221(chain B and (resid 6 through 33 or (resid 34...B34
231(chain B and (resid 6 through 33 or (resid 34...B6 - 259
241(chain B and (resid 6 through 33 or (resid 34...B6 - 259
251(chain B and (resid 6 through 33 or (resid 34...B6 - 259
261(chain B and (resid 6 through 33 or (resid 34...B6 - 259
311(chain C and (resid 6 through 33 or (resid 34...C6 - 33
321(chain C and (resid 6 through 33 or (resid 34...C34
331(chain C and (resid 6 through 33 or (resid 34...C6 - 261
341(chain C and (resid 6 through 33 or (resid 34...C6 - 261
351(chain C and (resid 6 through 33 or (resid 34...C6 - 261
361(chain C and (resid 6 through 33 or (resid 34...C6 - 261

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Components

#1: Protein Oxidoreductase


Mass: 30280.781 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain NCCP11945) (bacteria)
Strain: NCCP11945 / Gene: NGK_1143 / Plasmid: NegoA.00101.b.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4RLY3
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 3.14 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: JCSG+ D12 (274715d12): 40mM Potassium phosphate monobasic, 16% (w/v) PEG 8000, 20% (v/v) glycerol, protein conc. 18.5mg/mL, direct cryo, puck hat5-6

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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: Oct 26, 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: 2.5→50 Å / Num. obs: 39389 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 7.412 % / Biso Wilson estimate: 34.16 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Net I/σ(I): 15.07
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.5-2.567.570.4973.980.882199.8
2.56-2.647.5670.4214.730.916199.7
2.64-2.717.5610.3445.710.943199.6
2.71-2.87.5620.3186.180.951199.6
2.8-2.897.5530.2497.760.967199.8
2.89-2.997.5650.2268.580.973199.6
2.99-3.17.5430.17610.740.983199.4
3.1-3.237.5040.13414.060.988199.1
3.23-3.377.4860.11815.810.992199.2
3.37-3.547.4070.09918.40.993199.2
3.54-3.737.3060.08421.560.996199
3.73-3.957.2490.07823.270.994198.9
3.95-4.237.2140.07225.220.995198.2
4.23-4.567.0950.06726.570.996198.5
4.56-57.1110.06327.90.997197.9
5-5.597.2050.06327.170.997197.7
5.59-6.457.3380.06225.090.997197.7
6.45-7.917.2570.05626.690.997197.6
7.91-11.187.1110.0531.320.998196.5
11.18-506.4670.04730.230.997191

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3crz

3crz


Resolution: 2.5→50 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.03
RfactorNum. reflection% reflection
Rfree0.2204 2028 5.15 %
Rwork0.1746 --
obs0.1769 39386 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.67 Å2 / Biso mean: 37.3878 Å2 / Biso min: 1.73 Å2
Refinement stepCycle: final / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5765 0 303 195 6263
Biso mean--34.39 34.13 -
Num. residues----738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086257
X-RAY DIFFRACTIONf_angle_d1.0148539
X-RAY DIFFRACTIONf_chiral_restr0.059934
X-RAY DIFFRACTIONf_plane_restr0.0061241
X-RAY DIFFRACTIONf_dihedral_angle_d16.2563789
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3335X-RAY DIFFRACTION9.949TORSIONAL
12B3335X-RAY DIFFRACTION9.949TORSIONAL
13C3335X-RAY DIFFRACTION9.949TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.56250.27451520.216526412793100
2.5625-2.63180.26771430.210126262769100
2.6318-2.70920.25741400.208126742814100
2.7092-2.79670.28991480.209126502798100
2.7967-2.89660.27591620.202626252787100
2.8966-3.01250.2391400.206926772817100
3.0125-3.14960.24441330.195426602793100
3.1496-3.31560.25131400.18682650279099
3.3156-3.52320.23771760.18472638281499
3.5232-3.79510.22091620.16652655281799
3.7951-4.17660.19451300.15662670280098
4.1766-4.78020.17781330.1372702283598
4.7802-6.01950.15931450.15092684282998
6.0195-41.0530.19151240.16762806293097
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)
10.6995-0.553-0.96663.0305-0.02921.96590.3158-0.13620.06310.4835-0.1230.3020.03110.143-0.10090.2291-0.12140.09820.2578-0.09370.301839.0962-20.866623.1477
20.6387-0.20310.24591.3668-0.27741.09770.1042-0.15780.03260.1808-0.06510.49480.18670.124-0.03880.3034-0.08630.1060.2115-0.09360.378440.1565-27.06821.0879
30.5208-0.9081.29041.9364-2.53233.39060.12040.16460.0170.3694-0.3203-0.368-0.5960.88880.3480.2683-0.15980.06310.4923-0.08740.429853.355-11.411.2124
42.11610.67170.93923.58130.78362.8937-0.01830.04490.24560.0240.1950.0406-0.38190.1941-0.14860.2267-0.05710.05140.2306-0.09210.321740.1681-11.6255.929
53.3717-0.02850.65772.7724-1.69412.89890.02530.07460.41850.0333-0.03090.4676-0.24620.06210.00810.2753-0.04360.02350.2209-0.09450.3738.8081-11.912-3.2241
62.53811.4347-0.46843.8872-1.59372.58430.13790.3239-0.1317-0.13680.071-0.242-0.06950.3115-0.20260.1803-0.02850.05450.3766-0.17650.356453.8606-17.8007-0.9296
72.37180.33590.30331.50680.35722.2284-0.0243-0.339-0.02780.11190.1081-0.2078-0.1420.1896-0.09040.341-0.08070.11080.3066-0.07430.213543.05062.253145.1234
84.9647-1.48152.66662.075-0.55222.59490.19870.5069-0.8654-0.03210.1602-0.07270.29990.2056-0.1970.3131-0.05860.14580.3398-0.12340.411332.5997-11.886332.0752
92.0931-0.9833-0.00643.21681.64982.8146-0.02950.1507-0.1479-0.09160.01210.3184-0.2117-0.04690.00120.2528-0.02410.09230.2233-0.02360.252821.4909-1.83733.9153
102.97860.6033-1.22313.2341-0.5941.6483-0.06690.1295-0.5050.1667-0.2415-0.39730.09460.13380.2510.2086-0.13130.07690.3851-0.07340.31665.9686-1.117317.9176
116.2747-3.7401-1.99253.41762.19161.4995-0.1478-0.6176-0.021.18960.39740.474-0.30150.0498-0.04890.6689-0.11960.29770.3099-0.09920.350953.42038.842232.3855
123.57090.6915-0.88271.1207-1.02971.66740.40520.29820.17620.4105-0.20260.4725-0.2302-0.0927-0.15950.3475-0.1640.13690.3141-0.08570.324753.199814.712818.972
135.2751-0.9123-1.4282.256-0.47684.0830.27160.4340.42090.579-0.310.5703-0.4402-0.3504-0.00710.4333-0.12120.14530.3278-0.04680.376152.986923.925417.6635
140.6716-0.3064-0.64081.83970.72771.27920.4172-0.35330.24970.8999-0.25820.1564-0.83020.2831-0.32880.8811-0.37150.14460.4201-0.13660.207559.292221.535932.2646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 41 )A6 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 97 )A42 - 97
3X-RAY DIFFRACTION3chain 'A' and (resid 98 through 113 )A98 - 113
4X-RAY DIFFRACTION4chain 'A' and (resid 114 through 157 )A114 - 157
5X-RAY DIFFRACTION5chain 'A' and (resid 158 through 226 )A158 - 226
6X-RAY DIFFRACTION6chain 'A' and (resid 227 through 259 )A227 - 259
7X-RAY DIFFRACTION7chain 'B' and (resid 6 through 97 )B6 - 97
8X-RAY DIFFRACTION8chain 'B' and (resid 98 through 113 )B98 - 113
9X-RAY DIFFRACTION9chain 'B' and (resid 114 through 259 )B114 - 259
10X-RAY DIFFRACTION10chain 'C' and (resid 6 through 97 )C6 - 97
11X-RAY DIFFRACTION11chain 'C' and (resid 98 through 113 )C98 - 113
12X-RAY DIFFRACTION12chain 'C' and (resid 114 through 157 )C114 - 157
13X-RAY DIFFRACTION13chain 'C' and (resid 158 through 226 )C158 - 226
14X-RAY DIFFRACTION14chain 'C' and (resid 227 through 259 )C227 - 259

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