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- PDB-6qkr: 2-Naphthoyl-CoA Reductase-2-Naphthoyl-CoA complex(NCR-NCoA-soaked... -

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Basic information

Entry
Database: PDB / ID: 6qkr
Title2-Naphthoyl-CoA Reductase-2-Naphthoyl-CoA complex(NCR-NCoA-soaked complex)
ComponentsNCR
KeywordsFLAVOPROTEIN / Reductase / 2-Naphthoyl-CoA / 2-Naphthoyl-CoA Reductase / Naphthalene / FAD / FMN / 4Fe-4S / Hydride transfer / Monomer
Function / homology
Function and homology information


FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
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: 2.2 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: 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NCR
B: NCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,87110
Polymers155,8412
Non-polymers5,0308
Water4,396244
1
A: NCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4365
Polymers77,9201
Non-polymers2,5154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4365
Polymers77,9201
Non-polymers2,5154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.670, 86.050, 96.900
Angle α, β, γ (deg.)90.00, 90.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NCR


Mass: 77920.461 Da / Num. of mol.: 2
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, 252 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C32H42N7O17P3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 7.5
Details: PEG 4000/3350, NaF, Silver bullet solution A12/BioD4

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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: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 67546 / % possible obs: 99.7 % / Redundancy: 2 % / Biso Wilson estimate: 53.66 Å2 / CC1/2: 0.999 / Rsym value: 0.071 / Net I/σ(I): 20.7
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6488 / CC1/2: 0.875 / % possible all: 99.4

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Processing

Software
NameClassification
XDSdata reduction
PHASERphasing
ARP/wARPmodel building
Cootmodel building
PHENIXrefinement
BUSTERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6qkg

6qkg


Resolution: 2.2→30.24 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.248 / SU Rfree Blow DPI: 0.186 / SU Rfree Cruickshank DPI: 0.191
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3405 5.04 %RANDOM
Rwork0.178 ---
obs0.18 67546 99 %-
Displacement parametersBiso mean: 62.71 Å2
Baniso -1Baniso -2Baniso -3
1--4.4287 Å20 Å20.2751 Å2
2---7.0087 Å20 Å2
3---11.4374 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: 1 / Resolution: 2.2→30.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10151 0 304 244 10699
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110692HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.114506HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3756SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes259HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1649HARMONIC5
X-RAY DIFFRACTIONt_it10692HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion18.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1399SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12604SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 234 5.03 %
Rwork0.243 4415 -
all0.243 4649 -
obs--93.26 %
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)
10.85420.4354-0.40540.5074-0.4951.67730.0444-0.044-0.0251-0.0769-0.00930.00690.168-0.0636-0.03510.00380.04350.0413-0.0844-0.0178-0.1987-22.6089-4.0623-5.4382
20.94080.47950.40560.65440.25371.00040.1439-0.1128-0.0033-0.0606-0.1166-0.0666-0.1187-0.1132-0.0272-0.05560.0495-0.0222-0.01110.0192-0.1736-17.6154-44.6579-46.1379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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