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- PDB-6qkx: 2-Naphthoyl-CoA Reductase-DiHydroNaphthoyl-CoA complex(NCR-DHNCoA... -

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Basic information

Entry
Database: PDB / ID: 6qkx
Title2-Naphthoyl-CoA Reductase-DiHydroNaphthoyl-CoA complex(NCR-DHNCoA co-crystallized complex)
ComponentsNCR
KeywordsFLAVOPROTEIN / Reductase / 2-Naphthoyl-CoA / 2-Naphthoyl-CoA reductase / Naphthalene / FAD / FMN / [4Fe-4S] / Hydride transfer / Co-crystallized
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
Similarity search - Function
NAD(P)-binding Rossmann-like domain / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / Chem-J5H / IRON/SULFUR CLUSTER / NADH oxidase
Similarity search - Component
Biological speciesbacterium enrichment culture clone N47 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKayastha, K. / Ermler, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationRTG 1976, SPP 1927 Germany
CitationJournal: Nat Commun / Year: 2019
Title: Low potential enzymatic hydride transfer via highly cooperative and inversely functionalized flavin cofactors.
Authors: Willistein, M. / Bechtel, D.F. / Muller, C.S. / Demmer, U. / Heimann, L. / Kayastha, K. / Schunemann, V. / Pierik, A.J. / Ullmann, G.M. / Ermler, U. / Boll, M.
History
DepositionJan 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4365
Polymers77,9201
Non-polymers2,5154
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-36 kcal/mol
Surface area24320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.860, 176.860, 49.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NCR


Mass: 77920.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF4, FAD, FMN, LIG
Source: (gene. exp.) bacterium enrichment culture clone N47 (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: E1YD54

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Non-polymers , 5 types, 31 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical ChemComp-J5H / ~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] naphthalene-2-carbothioate


Mass: 921.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H42N7O17P3S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 7.5 / Details: PEG 3350, NaF

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 29947 / % possible obs: 99.1 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rsym value: 0.071 / Net I/σ(I): 12.9
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2975 / CC1/2: 0.895 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Cootmodel building
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6qkr

6qkr


Resolution: 2.4→47.418 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2735 1449 4.84 %
Rwork0.2291 --
obs0.2313 29947 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→47.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5064 0 152 27 5243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045317
X-RAY DIFFRACTIONf_angle_d0.9157212
X-RAY DIFFRACTIONf_dihedral_angle_d9.0643158
X-RAY DIFFRACTIONf_chiral_restr0.052789
X-RAY DIFFRACTIONf_plane_restr0.0071567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.48570.43571480.35212830X-RAY DIFFRACTION100
2.4857-2.58520.43371380.33472865X-RAY DIFFRACTION100
2.5852-2.70290.44851370.37022804X-RAY DIFFRACTION98
2.7029-2.84540.38191380.30612832X-RAY DIFFRACTION100
2.8454-3.02360.35131350.27222850X-RAY DIFFRACTION99
3.0236-3.2570.33241500.25932817X-RAY DIFFRACTION99
3.257-3.58470.29251380.25412846X-RAY DIFFRACTION99
3.5847-4.10320.25711310.21642850X-RAY DIFFRACTION98
4.1032-5.16850.23111640.18522850X-RAY DIFFRACTION100
5.1685-47.42720.22841700.19412955X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 2.3383 Å / Origin y: -27.9047 Å / Origin z: -9.1934 Å
111213212223313233
T0.8007 Å20.0237 Å2-0.0437 Å2-0.7818 Å20.1064 Å2--0.7734 Å2
L1.5759 °2-0.8995 °20.3289 °2-1.6907 °2-0.1898 °2--0.5992 °2
S-0.0275 Å °-0.0543 Å °0.032 Å °-0.0994 Å °0.1308 Å °1.0052 Å °-0.0166 Å °-0.2571 Å °-0.0859 Å °
Refinement TLS groupSelection details: all

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