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- PDB-6myw: Gluconobacter Ene-Reductase (GluER) mutant - T36A -

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Basic information

Entry
Database: PDB / ID: 6myw
TitleGluconobacter Ene-Reductase (GluER) mutant - T36A
ComponentsN-ethylmaleimide reductase
KeywordsOXIDOREDUCTASE / G OXYDANS / OLD YELLOW ENZYME / LACTAM CYCLASE / T36A GLUER
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
Similarity search - Function
Oxidoreductase Oye-like / 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
ACETATE ION / FLAVIN MONONUCLEOTIDE / N-ethylmaleimide reductase
Similarity search - Component
Biological speciesGluconobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.157 Å
AuthorsGarfinkle, S.E. / Jeffrey, P. / Hyster, T.K.
CitationJournal: Science / Year: 2019
Title: Photoexcitation of flavoenzymes enables a stereoselective radical cyclization.
Authors: Biegasiewicz, K.F. / Cooper, S.J. / Gao, X. / Oblinsky, D.G. / Kim, J.H. / Garfinkle, S.E. / Joyce, L.A. / Sandoval, B.A. / Scholes, G.D. / Hyster, T.K.
History
DepositionNov 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 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.ptnr2_symmetry / _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: N-ethylmaleimide reductase
B: N-ethylmaleimide reductase
C: N-ethylmaleimide reductase
D: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,58830
Polymers161,3134
Non-polymers3,27526
Water35,6341978
1
A: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0365
Polymers40,3281
Non-polymers7084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-21 kcal/mol
Surface area12780 Å2
MethodPISA
2
B: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0827
Polymers40,3281
Non-polymers7536
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-33 kcal/mol
Surface area13070 Å2
MethodPISA
3
C: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,33912
Polymers40,3281
Non-polymers1,01111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-68 kcal/mol
Surface area12960 Å2
MethodPISA
4
D: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1326
Polymers40,3281
Non-polymers8045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-29 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.475, 45.154, 163.744
Angle α, β, γ (deg.)90.00, 107.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
N-ethylmaleimide reductase / NADH oxidase


Mass: 40328.277 Da / Num. of mol.: 4 / Mutation: T36A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Gene: nox, AD934_01855, AD950_09540 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): pET22b / References: UniProt: A1E8I9

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Non-polymers , 6 types, 2004 molecules

#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1978 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100 MM SODIUM ACETATE MONOHYDRATE PH 4.6, 150 MM AMMONIUM SULFATE, 25% (W/V) PEG 4000
PH range: 4.2-5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.534
11-H, -K, H+L20.466
ReflectionResolution: 1.157→156 Å / Num. obs: 458784 / % possible obs: 95.2 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.026 / Rrim(I) all: 0.066 / Χ2: 0.93 / Net I/σ(I): 13.3
Reflection shellResolution: 1.157→1.18 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 19128 / CC1/2: 0.852 / Rpim(I) all: 0.276 / Rrim(I) all: 0.675 / Χ2: 0.96 / % possible all: 81

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimless0.7.2data scaling
PHENIX1.13-2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WJS

3wjs


Resolution: 1.157→29.28 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.447 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.006 / ESU R Free: 0.006
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESTRAINED ANISOTROPIC B-FACTORS ARE REFINED FOR PROTEIN AND FMN CO-FACTOR ATOMS, WITH ISOTROPIC B-FACTORS REFINED FOR SOLVENT MOLECULES.
RfactorNum. reflection% reflectionSelection details
Rfree0.1455 23052 5 %RANDOM
Rwork0.12315 ---
obs0.12426 435695 95.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å2-0.28 Å2
2--5.99 Å20 Å2
3----4.36 Å2
Refinement stepCycle: 1 / Resolution: 1.157→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10940 0 203 1978 13121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01311471
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710450
X-RAY DIFFRACTIONr_angle_refined_deg1.9781.66815630
X-RAY DIFFRACTIONr_angle_other_deg1.6271.58424224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73351434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88821.452613
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.583151764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2231594
X-RAY DIFFRACTIONr_chiral_restr0.120.21491
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0213026
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022452
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1681.0415731
X-RAY DIFFRACTIONr_mcbond_other1.1611.4645726
X-RAY DIFFRACTIONr_mcangle_it1.2881.577164
X-RAY DIFFRACTIONr_mcangle_other1.294.5037165
X-RAY DIFFRACTIONr_scbond_it1.8391.2015740
X-RAY DIFFRACTIONr_scbond_other1.8391.2015741
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0051.7448467
X-RAY DIFFRACTIONr_long_range_B_refined2.24613789
X-RAY DIFFRACTIONr_long_range_B_other1.82413310
X-RAY DIFFRACTIONr_rigid_bond_restr4.172311414
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.157→1.187 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 1494 -
Rwork0.152 28283 -
obs--83.77 %

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