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- PDB-3s2f: Crystal Structure of FurX NADH:Furfural -

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Basic information

Entry
Database: PDB / ID: 3s2f
TitleCrystal Structure of FurX NADH:Furfural
ComponentsZinc-containing alcohol dehydrogenase superfamily
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / FurX
Function / homology
Function and homology information


alcohol dehydrogenase / oxidoreductase activity / nucleotide binding / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FURFURAL / PHOSPHORYLISOPROPANE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / alcohol dehydrogenase
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHayes, R. / Sanchez, E.J. / Webb, B.N. / Hooper, T. / Nissen, M.S. / Li, Q. / Xun, L.
CitationJournal: To be Published
Title: Crystal structures and furfural reduction mechanism of a bacterial zinc-dependent alcohol dehydrogenase
Authors: Hayes, R. / Sanchez, E.J. / Webb, B.N. / Hooper, T. / Nissen, M.S. / Li, Q. / Xun, L.
History
DepositionMay 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 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_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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc-containing alcohol dehydrogenase superfamily
B: Zinc-containing alcohol dehydrogenase superfamily
C: Zinc-containing alcohol dehydrogenase superfamily
D: Zinc-containing alcohol dehydrogenase superfamily
E: Zinc-containing alcohol dehydrogenase superfamily
F: Zinc-containing alcohol dehydrogenase superfamily
G: Zinc-containing alcohol dehydrogenase superfamily
H: Zinc-containing alcohol dehydrogenase superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,09250
Polymers286,1028
Non-polymers5,99042
Water40,0832225
1
A: Zinc-containing alcohol dehydrogenase superfamily
D: Zinc-containing alcohol dehydrogenase superfamily
F: Zinc-containing alcohol dehydrogenase superfamily
G: Zinc-containing alcohol dehydrogenase superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,04625
Polymers143,0514
Non-polymers2,99521
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14830 Å2
ΔGint-179 kcal/mol
Surface area47090 Å2
MethodPISA
2
B: Zinc-containing alcohol dehydrogenase superfamily
C: Zinc-containing alcohol dehydrogenase superfamily
E: Zinc-containing alcohol dehydrogenase superfamily
H: Zinc-containing alcohol dehydrogenase superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,04625
Polymers143,0514
Non-polymers2,99521
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14840 Å2
ΔGint-182 kcal/mol
Surface area47040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.271, 92.854, 117.690
Angle α, β, γ (deg.)106.080, 89.970, 89.980
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Zinc-containing alcohol dehydrogenase superfamily


Mass: 35762.754 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: JMP134 / LMG 1197 / Gene: Reut_B3677 / Production host: Escherichia coli (E. coli) / References: UniProt: Q46UZ9

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Non-polymers , 6 types, 2267 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ISP / PHOSPHORYLISOPROPANE


Mass: 140.075 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H9O4P
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#6: Chemical
ChemComp-FU2 / FURFURAL


Mass: 96.084 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2225 / 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: 2.51 Å3/Da / Density % sol: 50.91 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.88→46 Å / Num. all: 209479 / Num. obs: 166925 / % possible obs: 89 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→45.984 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8576 / SU ML: 0.24 / σ(F): 0.08 / Phase error: 22.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2138 1558 93 %
Rwork0.1818 --
obs0.1821 166925 88.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.151 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 109.47 Å2 / Biso mean: 26.0212 Å2 / Biso min: 8.74 Å2
Baniso -1Baniso -2Baniso -3
1-2.2468 Å20.5191 Å20.6619 Å2
2---1.7967 Å21.7509 Å2
3----0.4501 Å2
Refinement stepCycle: LAST / Resolution: 2→45.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20120 0 306 2225 22651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00320832
X-RAY DIFFRACTIONf_angle_d0.95428388
X-RAY DIFFRACTIONf_chiral_restr0.0873212
X-RAY DIFFRACTIONf_plane_restr0.0033684
X-RAY DIFFRACTIONf_dihedral_angle_d14.1697568
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.06460.2671220.2598124871260974
2.0646-2.13830.30181140.2471134981361280
2.1383-2.2240.31691360.2287141761431284
2.224-2.32520.26381430.2196142831442685
2.3252-2.44780.27961360.1986149611509788
2.4478-2.60110.26461370.199150461518389
2.6011-2.80190.20291480.1884156041575292
2.8019-3.08380.22681440.1844159601610494
3.0838-3.52990.18761600.1719162531641396
3.5299-4.44670.16991610.1427164691663097
4.4467-45.99620.17671570.1574166301678798

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