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- PDB-6c75: Structure of Iron containing alcohol dehydrogenase from Thermococ... -

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Basic information

Entry
Database: PDB / ID: 6c75
TitleStructure of Iron containing alcohol dehydrogenase from Thermococcus thioreducens in a monoclinic 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 / 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
2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Alcohol dehydrogenase
Similarity search - Component
Biological speciesThermococcus thioreducens (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 19, 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)84,4465
Polymers83,1402
Non-polymers1,3063
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-49 kcal/mol
Surface area28620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.125, 99.248, 67.487
Angle α, β, γ (deg.)90.00, 103.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


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 / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-ATR / 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M Sodium acetate, 8% PEG 4000, pH 4.5

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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 11, 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: 2.4→49.61 Å / Num. obs: 23385 / % possible obs: 79 % / Redundancy: 6.5 % / Biso Wilson estimate: 48.6 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.234 / Rpim(I) all: 0.092 / Rrim(I) all: 0.253 / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 677 / CC1/2: 0.368 / Rpim(I) all: 0.646 / Rrim(I) all: 0.993 / % possible all: 22

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLM7.1.0data reduction
Aimless0.5.1data scaling
PHASER2.5.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O2D

1o2d


Resolution: 2.4→49.61 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.931 / SU B: 21.131 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.288 / Stereochemistry target values: Maximum Likelihood
Details: HYDROGENS WERE GENERATED BY REFMAC5 AND KEPT IN POSITION BY RIDING ON THE ATOMS TO WHICH THEY WERE ATTACHED UNLESS MOVED TO RELIEVE VAN DER WAALS CONTACTS
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 1150 4.9 %RANDOM
Rwork0.14311 ---
obs0.14636 22218 78.88 %-
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: 66.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å2-0 Å22.47 Å2
2---0.5 Å20 Å2
3----2.04 Å2
Refinement stepCycle: 1 / Resolution: 2.4→49.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5852 0 80 167 6099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0196065
X-RAY DIFFRACTIONr_bond_other_d00.026009
X-RAY DIFFRACTIONr_angle_refined_deg0.6152.0038224
X-RAY DIFFRACTIONr_angle_other_deg0.496313750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9835754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9723.417240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.673151048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3531540
X-RAY DIFFRACTIONr_chiral_restr0.040.2918
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0216668
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021277
X-RAY DIFFRACTIONr_nbd_refined0.2210.22908
X-RAY DIFFRACTIONr_nbd_other0.2080.211330
X-RAY DIFFRACTIONr_nbtor_refined0.1880.25910
X-RAY DIFFRACTIONr_nbtor_other0.0930.25660
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2186
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0340.28
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6034.9733022
X-RAY DIFFRACTIONr_mcbond_other3.6034.9713021
X-RAY DIFFRACTIONr_mcangle_it5.4137.4513774
X-RAY DIFFRACTIONr_mcangle_other5.4127.4533775
X-RAY DIFFRACTIONr_scbond_it4.7065.8563043
X-RAY DIFFRACTIONr_scbond_other4.7015.8523035
X-RAY DIFFRACTIONr_scangle_it7.5148.4954450
X-RAY DIFFRACTIONr_scangle_other7.5088.4884438
X-RAY DIFFRACTIONr_long_range_B_refined9.80441.0586828
X-RAY DIFFRACTIONr_long_range_B_other9.80741.0166802
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.403→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 21 -
Rwork0.298 402 -
obs--19.35 %
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)
10.32470.04610.00380.6874-0.18971.0665-0.10850.01280.0289-0.0050.12430.03680.06910.2177-0.01580.14990.0079-0.02780.1416-0.00720.035418.317868.85896.3504
20.4791-0.1639-0.38620.3512-0.00280.6254-0.13320.0896-0.12290.05760.04230.14330.03260.02930.09090.1465-0.0146-0.02270.1288-0.00920.1018-2.227854.56938.9515
30.3203-0.2113-0.46840.71510.14440.92650.0856-0.15980.0504-0.04310.07540.0884-0.05230.2674-0.16090.1251-0.0146-0.01240.1622-0.05620.0527.324685.551835.8304
40.7174-0.0357-0.3890.9511-0.10170.76140.01350.04870.0825-0.0201-0.04980.2088-0.06040.04510.03630.10690.0009-0.07580.0691-0.00620.146-15.112388.599522.815
50.4446-0.38031.49587.96961.00025.74850.0138-0.0934-0.00520.20370.0099-0.00950.1833-0.4019-0.02370.2463-0.0276-0.02030.1766-0.01540.00679.988362.05960.0923
611.7428-3.3848-0.24230.97670.07160.0078-0.0452-0.24290.24460.0010.0567-0.0735-0.0148-0.0166-0.01140.3524-0.00920.01680.28540.0070.0644-6.662584.988941.4546
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
6X-RAY DIFFRACTION6B1800

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