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- PDB-6c76: Structure of Iron containing alcohol dehydrogenase from Thermococ... -

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Basic information

Entry
Database: PDB / ID: 6c76
TitleStructure of Iron containing alcohol dehydrogenase from Thermococcus thioreducens in an orthorhombic crystal form
ComponentsAlcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Alcohol dehydrogenase / Iron-containing / OGL-20P
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / nucleotide binding / metal ion binding
Similarity search - Function
NADPH-dependent butanol dehydrogenase / Iron-type alcohol dehydrogenase-like / : / Fe-containing alcohol dehydrogenase family, C-terminal / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TRIETHYLENE GLYCOL / Alcohol dehydrogenase
Similarity search - Component
Biological speciesThermococcus thioreducens (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLarson, S.B. / McPherson, A.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2019
Title: The structure of an iron-containing alcohol dehydrogenase from a hyperthermophilic archaeon in two chemical states.
Authors: Larson, S.B. / Jones, J.A. / McPherson, A.
History
DepositionJan 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 4, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase
B: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1496
Polymers83,1402
Non-polymers1,0094
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-32 kcal/mol
Surface area28130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.920, 111.978, 142.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase


Mass: 41569.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus thioreducens (archaea) / Gene: AMR53_06445, SAMN05216170_0411 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Q2QQL1

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Non-polymers , 5 types, 297 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate, 10% PEG 10,000 at pH 4.6

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 18, 2013 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.1→43.97 Å / Num. obs: 41831 / % possible obs: 90 % / Redundancy: 20.4 % / Biso Wilson estimate: 36.7 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.041 / Rrim(I) all: 0.214 / Net I/σ(I): 13
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.974 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1309 / CC1/2: 0.222 / Rpim(I) all: 0.67 / Rrim(I) all: 1.192 / % possible all: 35.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLM7.1.0data reduction
Aimless0.5.1data scaling
PHASER2.2.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C75

6c75


Resolution: 2.1→33.04 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.945 / SU B: 13.459 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.181 / Stereochemistry target values: Maximum Likelihood
Details: HYDROGENS WERE GENERATED BY REFMAC AND ALLOWED TO RIDE ON THE ATOMS TO WHICH THEY WERE ATTACHED UNLESS MOVED TO RELIEVE VAN DER WAALS CONTACTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20419 2018 4.8 %RANDOM
Rwork0.15387 ---
obs0.15633 39750 89.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: Babinet Model with mask
Displacement parametersBiso mean: 46.619 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.98 Å2-0 Å2
3----0.95 Å2
Refinement stepCycle: 1 / Resolution: 2.1→33.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5852 0 63 293 6208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0196196
X-RAY DIFFRACTIONr_bond_other_d0.0040.026253
X-RAY DIFFRACTIONr_angle_refined_deg0.96428383
X-RAY DIFFRACTIONr_angle_other_deg0.618314314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4425771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97923.113257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.033151123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0111549
X-RAY DIFFRACTIONr_chiral_restr0.0610.2927
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0216798
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021319
X-RAY DIFFRACTIONr_nbd_refined0.2350.23388
X-RAY DIFFRACTIONr_nbd_other0.1990.212086
X-RAY DIFFRACTIONr_nbtor_refined0.1910.26156
X-RAY DIFFRACTIONr_nbtor_other0.0890.26648
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2232
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0540.28
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.237
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2880.28
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0880.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.463.523041
X-RAY DIFFRACTIONr_mcbond_other3.4533.5183039
X-RAY DIFFRACTIONr_mcangle_it4.9955.2733800
X-RAY DIFFRACTIONr_mcangle_other4.9975.2753801
X-RAY DIFFRACTIONr_scbond_it4.8624.3623155
X-RAY DIFFRACTIONr_scbond_other4.8624.3623156
X-RAY DIFFRACTIONr_scangle_it7.7376.2394574
X-RAY DIFFRACTIONr_scangle_other7.7376.2414575
X-RAY DIFFRACTIONr_long_range_B_refined10.529.8787281
X-RAY DIFFRACTIONr_long_range_B_other10.47829.7237211
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 55 -
Rwork0.349 1057 -
obs--32.73 %
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)
10.5645-0.1317-0.14730.2609-0.24020.45570.0401-0.00830.03730.01570.00540.0022-0.0470.0503-0.04550.0391-0.0105-0.00180.0321-0.02440.053830.323475.930946.5517
20.255-0.1126-0.20170.1897-0.15440.6866-0.0389-0.01730.0003-0.00880.0617-0.00730.1573-0.0626-0.02280.0816-0.0022-0.01830.0298-0.01170.020621.220553.054351.3569
31.0084-0.3080.15510.45240.43370.70480.00460.08940.0864-0.1404-0.10360.017-0.2137-0.07550.09910.10480.049-0.05040.0569-0.00280.040714.669372.714114.7182
40.44220.0022-0.04970.2044-0.0260.7056-0.0297-0.02090.0454-0.0858-0.00460.04360.07320.04060.03430.1014-0.0072-0.02220.00640.00040.017127.648750.337513.3161
55.98740.52022.00940.2187-0.3132.05770.1139-0.31620.1352-0.0273-0.07230.03750.11870.0024-0.04150.07480.0072-0.00040.0364-0.00990.04732.495265.514953.079
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 182
2X-RAY DIFFRACTION2A183 - 378
3X-RAY DIFFRACTION3B1 - 182
4X-RAY DIFFRACTION4B183 - 378
5X-RAY DIFFRACTION5A402

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