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- PDB-6uff: Structure of Ene-reductase 1 NostocER1 from cyanobacteria -

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Basic information

Entry
Database: PDB / ID: 6uff
TitleStructure of Ene-reductase 1 NostocER1 from cyanobacteria
ComponentsEne-reductase 1
KeywordsOXIDOREDUCTASE / ENE REDUCTASE / CYANOBACTERIA / ALKENE REDUCTASE
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
Similarity search - Function
NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / All1865 protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.007 Å
AuthorsSandoval, B. / Jeffrey, P.D. / Hyster, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Photoenzymatic Hydrogenation of Heteroaromatic Olefins Using 'Ene'-Reductases with Photoredox Catalysts.
Authors: Nakano, Y. / Black, M.J. / Meichan, A.J. / Sandoval, B.A. / Chung, M.M. / Biegasiewicz, K.F. / Zhu, T. / Hyster, T.K.
History
DepositionSep 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3Oct 11, 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_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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: Ene-reductase 1
B: Ene-reductase 1
C: Ene-reductase 1
D: Ene-reductase 1
E: Ene-reductase 1
F: Ene-reductase 1
G: Ene-reductase 1
H: Ene-reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,26828
Polymers360,1368
Non-polymers4,13220
Water29,8331656
1
A: Ene-reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5544
Polymers45,0171
Non-polymers5373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ene-reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5133
Polymers45,0171
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ene-reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5544
Polymers45,0171
Non-polymers5373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ene-reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5544
Polymers45,0171
Non-polymers5373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ene-reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5544
Polymers45,0171
Non-polymers5373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Ene-reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5133
Polymers45,0171
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Ene-reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5133
Polymers45,0171
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Ene-reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5133
Polymers45,0171
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.565, 95.589, 99.903
Angle α, β, γ (deg.)66.79, 89.91, 82.58
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Ene-reductase 1


Mass: 45017.008 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: all1865 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8YVV8
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1656 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.97 Å3/Da / Density % sol: 37.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1M Tricine HCl pH 9.0, 0.1-0.2M CaCl2, 28-30% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97895 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 18, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2→90 Å / Num. obs: 178989 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.12 / Net I/σ(I): 8.73
Reflection shellResolution: 2.01→2.13 Å / Redundancy: 3.37 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 1.63 / Num. unique obs: 28111 / CC1/2: 0.644 / Rrim(I) all: 0.796 / % possible all: 94.5

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Processing

Software
NameClassificationNB
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GKA

3gka


Resolution: 2.007→29.522 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 9132 5.1 %Random
Rwork0.1731 ---
obs0.1757 178926 97.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.007→29.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22180 0 260 1656 24096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723058
X-RAY DIFFRACTIONf_angle_d0.91931403
X-RAY DIFFRACTIONf_dihedral_angle_d13.8358269
X-RAY DIFFRACTIONf_chiral_restr0.0363441
X-RAY DIFFRACTIONf_plane_restr0.0054166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.007-2.02980.35042500.28525126X-RAY DIFFRACTION86
2.0298-2.05370.2973250.26955584X-RAY DIFFRACTION97
2.0537-2.07880.29663020.25145617X-RAY DIFFRACTION97
2.0788-2.10510.29773140.23815539X-RAY DIFFRACTION97
2.1051-2.13280.26972720.23415708X-RAY DIFFRACTION97
2.1328-2.1620.28993250.23025590X-RAY DIFFRACTION97
2.162-2.19280.28433220.21855638X-RAY DIFFRACTION97
2.1928-2.22560.2853240.20885655X-RAY DIFFRACTION97
2.2256-2.26030.27222880.21175666X-RAY DIFFRACTION97
2.2603-2.29740.26242920.2015588X-RAY DIFFRACTION97
2.2974-2.3370.25713110.19945740X-RAY DIFFRACTION97
2.337-2.37940.27382800.20395604X-RAY DIFFRACTION97
2.3794-2.42520.2763010.20125678X-RAY DIFFRACTION98
2.4252-2.47470.25632780.18895713X-RAY DIFFRACTION98
2.4747-2.52840.26232920.18795679X-RAY DIFFRACTION98
2.5284-2.58720.24432900.18755736X-RAY DIFFRACTION98
2.5872-2.65190.2383050.17875680X-RAY DIFFRACTION98
2.6519-2.72350.23572880.18345770X-RAY DIFFRACTION98
2.7235-2.80360.22033200.17045663X-RAY DIFFRACTION98
2.8036-2.8940.23433010.17225694X-RAY DIFFRACTION98
2.894-2.99740.21213430.17695709X-RAY DIFFRACTION98
2.9974-3.11730.26153000.17415700X-RAY DIFFRACTION98
3.1173-3.2590.21543420.16725694X-RAY DIFFRACTION98
3.259-3.43060.21672770.16455710X-RAY DIFFRACTION98
3.4306-3.64510.20493220.16075657X-RAY DIFFRACTION98
3.6451-3.9260.19413250.1515720X-RAY DIFFRACTION98
3.926-4.320.17723160.13665690X-RAY DIFFRACTION98
4.32-4.94260.16393090.12855733X-RAY DIFFRACTION99
4.9426-6.21750.18353010.14465790X-RAY DIFFRACTION99
6.2175-29.52480.18363170.15995723X-RAY DIFFRACTION99

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