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- PDB-5tr9: Crystal Structure of a ferredoxin NADP+ reductase from Neisseria ... -

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Basic information

Entry
Database: PDB / ID: 5tr9
TitleCrystal Structure of a ferredoxin NADP+ reductase from Neisseria gonorrhoeae with bound FAD
ComponentsFerredoxin-NADP reductase
KeywordsOXIDOREDUCTASE / SSGCID / Neisseria gonorrhoeae / ferredoxin NADP+ reductase / FAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


ferredoxin-NADP+ reductase activity / nucleotide binding / metal ion 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 / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae MIA_2011_03-10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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
Authors: Mayclin, S.J. / Fox III, D. / Lorimer, D.D. / Edwards, T.E.
History
DepositionOct 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_oper_list / reflns_shell / software
Item: _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all
Revision 1.2Oct 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_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)63,69243
Polymers60,5622
Non-polymers3,13141
Water11,980665
1
A: Ferredoxin-NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,90623
Polymers30,2811
Non-polymers1,62522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferredoxin-NADP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,78620
Polymers30,2811
Non-polymers1,50519
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.010, 163.010, 163.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21A-732-

HOH

31A-745-

HOH

41A-748-

HOH

51B-699-

HOH

61B-712-

HOH

71B-713-

HOH

81B-715-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ferredoxin-NADP reductase


Mass: 30280.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NegoA.00101.b.B1
Source: (gene. exp.) Neisseria gonorrhoeae MIA_2011_03-10 (bacteria)
Gene: M736_10480 / Plasmid: NegoA.00101.b.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3GZJ1

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Non-polymers , 6 types, 706 molecules

#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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / 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: 2.99 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MCSG1 A4 (274714a4): 200mM MgCl2, 100mM Tris-HCl pH7.0, 2500mM NaCl, protein conc. 18.5mg/mL, cryo 20% v/v ethylene glycol, puck lhk6-1

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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 8, 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: 1.65→47.057 Å / Num. obs: 86081 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 15.1 % / Biso Wilson estimate: 16.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.8
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.65-1.690.5415.340.943199.8
1.69-1.740.4426.460.9581100
1.74-1.790.3617.750.973199.9
1.79-1.840.2889.580.9821100
1.84-1.910.22811.840.9881100
1.91-1.970.19313.770.9911100
1.97-2.050.16116.180.993199.8
2.05-2.130.13818.570.9951100
2.13-2.220.12320.260.995199.9
2.22-2.330.11122.410.9961100
2.33-2.460.10523.830.9961100
2.46-2.610.09725.460.9961100
2.61-2.790.09127.320.997199.8
2.79-3.010.08529.210.9971100
3.01-3.30.0831.630.9971100
3.3-3.690.07733.890.997199.9
3.69-4.260.07534.720.9971100
4.26-5.220.07435.270.9971100
5.22-7.380.07634.230.997199.8
7.380.07634.220.997199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3crz


Resolution: 1.65→47.057 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.51
RfactorNum. reflection% reflection
Rfree0.163 1995 2.32 %
Rwork0.1483 --
obs0.1486 86072 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.28 Å2 / Biso mean: 22.5225 Å2 / Biso min: 8.15 Å2
Refinement stepCycle: final / Resolution: 1.65→47.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3892 0 173 681 4746
Biso mean--21.68 35.73 -
Num. residues----492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064353
X-RAY DIFFRACTIONf_angle_d0.885917
X-RAY DIFFRACTIONf_chiral_restr0.059642
X-RAY DIFFRACTIONf_plane_restr0.006752
X-RAY DIFFRACTIONf_dihedral_angle_d16.2042599
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
1.65-1.69130.19941470.17159666113
1.6913-1.7370.16771270.164359456072
1.737-1.78810.1961510.169159846135
1.7881-1.84580.19571370.16159256062
1.8458-1.91180.14681310.153860236154
1.9118-1.98840.16431500.150460146164
1.9884-2.07890.16521410.148759586099
2.0789-2.18850.18551180.155359756093
2.1885-2.32560.18321440.149960256169
2.3256-2.50510.20431470.156859686115
2.5051-2.75720.17751570.16160186175
2.7572-3.15610.16311490.157460106159
3.1561-3.9760.13971800.126860496229
3.976-47.07610.12991160.136862176333
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)
11.2552-0.4131-0.52990.95690.36820.9996-0.0993-0.0522-0.11970.06110.0105-0.0420.16990.09690.08570.085-0.00030.01380.08970.01080.1163-17.7685-41.229139.7675
21.16580.4474-0.95471.5576-1.00092.50690.00150.1760.09910.01720.02850.1384-0.0579-0.2572-0.03060.06350.0043-0.01270.1383-0.0070.1208-29.182-22.152936.6441
31.9006-0.1355-0.6352.26970.14922.3720.004-0.1270.02950.1618-0.07910.0103-0.1289-0.0140.05780.0943-0.0318-0.01970.1018-0.0080.0914-24.4502-19.360250.5468
48.89642.29372.71166.35510.98944.6379-0.09570.13510.3934-0.0325-0.01360.0895-0.33530.19530.12460.12830.0230.06010.12590.00830.0146-5.52845.431922.759
51.61040.45110.11722.51770.291.40940.1889-0.34860.02950.1638-0.2451-0.1376-0.12240.24550.02660.1089-0.0110.01410.18440.05620.0961-1.0173-0.047523.944
61.29341.197-1.18834.1691-1.75973.2110.15390.11570.0022-0.2471-0.20820.03180.00340.12460.02410.09860.04890.02450.1370.04680.1105-3.4301-1.876215.1249
70.9005-0.08370.07573.0964-1.00422.16850.0271-0.1239-0.18760.1778-0.0550.1288-0.1286-0.02040.03460.1230.00230.02490.14540.02840.1082-7.8046-0.291430.036
80.7455-0.1384-0.44572.91870.42431.13530.02180.10780.0101-0.1534-0.0234-0.16880.09360.2601-0.0140.11420.05650.02850.21260.06740.15815.1662-11.98811.4684
92.68081.4481-1.01852.0711-0.96081.48930.01450.16810.0197-0.2513-0.0490.01050.11590.25340.01030.1230.05680.0110.19420.04560.1111-3.0031-15.35378.9746
103.83631.0564-0.9673.2383-0.84365.1637-0.04510.3555-0.1898-0.3594-0.0439-0.08530.2151-0.28510.04970.15720.03020.00090.1566-0.0270.1287-7.5862-25.063810.8541
112.4358-0.6965-0.58261.4627-0.11731.1260.09640.1386-0.2032-0.0882-0.1389-0.05380.0702-0.00290.0460.12630.04540.02050.15530.05870.17229.219-22.674414.7225
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 121 )A14 - 121
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 218 )A122 - 218
3X-RAY DIFFRACTION3chain 'A' and (resid 219 through 267 )A219 - 267
4X-RAY DIFFRACTION4chain 'B' and (resid 14 through 27 )B14 - 27
5X-RAY DIFFRACTION5chain 'B' and (resid 28 through 67 )B28 - 67
6X-RAY DIFFRACTION6chain 'B' and (resid 68 through 82 )B68 - 82
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 105 )B83 - 105
8X-RAY DIFFRACTION8chain 'B' and (resid 106 through 140 )B106 - 140
9X-RAY DIFFRACTION9chain 'B' and (resid 141 through 165 )B141 - 165
10X-RAY DIFFRACTION10chain 'B' and (resid 166 through 218 )B166 - 218
11X-RAY DIFFRACTION11chain 'B' and (resid 219 through 267 )B219 - 267

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