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- PDB-1jay: Structure of Coenzyme F420H2:NADP+ Oxidoreductase (FNO) with its ... -

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Basic information

Entry
Database: PDB / ID: 1jay
TitleStructure of Coenzyme F420H2:NADP+ Oxidoreductase (FNO) with its substrates bound
ComponentsCoenzyme F420H2:NADP+ Oxidoreductase (FNO)
KeywordsSTRUCTURAL GENOMICS / Rossmann fold
Function / homology
Function and homology information


8-hydroxy-5-deazaflavin:NADPH oxidoreductase / 8-hydroxy-5-deazaflavin:NADPH oxidoreductase activity / ferric-chelate reductase (NADPH) activity / coenzyme F420 binding / cupric reductase (NADH) activity / copper ion import / NADPH regeneration / oxidoreductase activity, acting on NAD(P)H / NADP binding / plasma membrane
Similarity search - Function
NADPH-dependent F420 reductase / : / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME F420 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / F420-dependent NADP reductase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWarkentin, E. / Mamat, B. / Thauer, R. / Ermler, U. / Shima, S.
CitationJournal: EMBO J. / Year: 2001
Title: Structures of F420H2:NADP+ oxidoreductase with and without its substrates bound.
Authors: Warkentin, E. / Mamat, B. / Sordel-Klippert, M. / Wicke, M. / Thauer, R.K. / Iwata, M. / Iwata, S. / Ermler, U. / Shima, S.
History
DepositionJun 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coenzyme F420H2:NADP+ Oxidoreductase (FNO)
B: Coenzyme F420H2:NADP+ Oxidoreductase (FNO)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8698
Polymers45,7892
Non-polymers3,0806
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-42 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.9, 69.8, 145.5
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 Coenzyme F420H2:NADP+ Oxidoreductase (FNO)


Mass: 22894.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF0892 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O29370
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-F42 / COENZYME F420


Mass: 773.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H36N5O18P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes pH7.5, 1.4 M tri-Na citrate, 1 mM F420, 1 mM NADP, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlenzyme1drop
21 mMF4201drop
31 mMNADP1drop
40.1 MHEPES-NaOH1reservoirpH7.5
51.4 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.957 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2000
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.957 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. all: 61974 / Num. obs: 61974 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.3
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.35 / Num. unique all: 3849 / % possible all: 72.4
Reflection
*PLUS
Num. obs: 58452
Reflection shell
*PLUS
Lowest resolution: 1.8 Å / % possible obs: 73.2 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FNO

Resolution: 1.65→29.45 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1288595.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2929 5 %RANDOM
Rwork0.182 ---
all0.182 58152 --
obs0.182 58152 85.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.62 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.99 Å20 Å20 Å2
2--1.19 Å20 Å2
3----4.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.65→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3289 0 204 324 3817
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.65-1.750.2913505.20.27363680.016665760
2.08-2.240.193010.176648295.8
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.59
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.15
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.291 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.273

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