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- PDB-6c7l: Structure of Iron containing alcohol dehydrogenase from Thermococ... -

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Basic information

Entry
Database: PDB / ID: 6c7l
TitleStructure of Iron containing alcohol dehydrogenase from Thermococcus thioreducens in a tetragonal 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 / PHOSPHATE ION / Alcohol dehydrogenase
Similarity search - Component
Biological speciesThermococcus thioreducens (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsJones, J.A. / Larson, 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 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,06223
Polymers41,5701
Non-polymers2,49222
Water8,323462
1
A: Alcohol dehydrogenase
hetero molecules

A: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,12446
Polymers83,1402
Non-polymers4,98444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area13150 Å2
ΔGint-323 kcal/mol
Surface area27850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.304, 69.304, 166.644
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-603-

HOH

21A-642-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alcohol dehydrogenase


Mass: 41569.961 Da / Num. of mol.: 1
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, 484 molecules

#2: Chemical ChemComp-ATR / 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.41 Å3/Da / Density % sol: 48.89 % / Description: tetragonal bipyramids
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 0.4 M NH4H2PO4, pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 20, 2014 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.909→29 Å / Num. obs: 30956 / % possible obs: 95.2 % / Redundancy: 20.7 % / Biso Wilson estimate: 28.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.02 / Rrim(I) all: 0.098 / Net I/σ(I): 12.5
Reflection shellResolution: 1.909→1.93 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1343 / CC1/2: 0.647 / Rpim(I) all: 0.355 / Rrim(I) all: 0.768 / % possible all: 84.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-3000data reduction
HKL-3000data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C76

6c76


Resolution: 1.91→29 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.414 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.136 / Stereochemistry target values: Maximum Likelihood
Details: HYDROGENS WERE GENERATED IN REFMAC AND ALLOWED TO RIDE THE ATOMS TO WHICH THEY WERE ATTACHED IN IDEAL POSITIONS EXCEPT WHERE VAN DER WAALS CONTACTS ALTERED THEIR POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18939 1997 6.5 %RANDOM
Rwork0.13668 ---
obs0.14011 28792 94.83 %-
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: 42.895 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å2-0 Å2
2--0.13 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.91→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 138 462 3526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193378
X-RAY DIFFRACTIONr_bond_other_d0.0010.023381
X-RAY DIFFRACTIONr_angle_refined_deg1.1222.0284616
X-RAY DIFFRACTIONr_angle_other_deg0.67937778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2585425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22523.475141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11815628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7791525
X-RAY DIFFRACTIONr_chiral_restr0.0750.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213601
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02713
X-RAY DIFFRACTIONr_nbd_refined0.2470.22612
X-RAY DIFFRACTIONr_nbd_other0.1720.26562
X-RAY DIFFRACTIONr_nbtor_refined0.1850.23140
X-RAY DIFFRACTIONr_nbtor_other0.0840.23356
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2174
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0450.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.2115
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1740.2133
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2223.1191570
X-RAY DIFFRACTIONr_mcbond_other2.223.1161569
X-RAY DIFFRACTIONr_mcangle_it3.0334.6671976
X-RAY DIFFRACTIONr_mcangle_other3.0344.671977
X-RAY DIFFRACTIONr_scbond_it3.4253.8611808
X-RAY DIFFRACTIONr_scbond_other3.4243.8651809
X-RAY DIFFRACTIONr_scangle_it5.2355.6172617
X-RAY DIFFRACTIONr_scangle_other5.2345.6212618
X-RAY DIFFRACTIONr_long_range_B_refined9.38929.0444315
X-RAY DIFFRACTIONr_long_range_B_other9.38829.0614316
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.909→1.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 127 -
Rwork0.286 1774 -
obs--80.76 %
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)
10.14020.10070.0040.1576-0.10860.75490.04320.0059-0.0747-0.00680.00870.00660.0861-0.0159-0.05190.072-0.0062-0.05850.02650.0010.0863-6.7881-31.4652-3.0062
20.20640.0331-0.16060.8025-0.20930.5710.06190.0319-0.0441-0.077-0.0494-0.1373-0.0630.026-0.01250.0384-0.01150.00160.08560.00940.07046.5261-11.8891-13.9998
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 182
2X-RAY DIFFRACTION2A183 - 378

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