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- PDB-5yvm: Crystal Structure of the archaeal halo-thermophilic Red Sea brine... -

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Basic information

Entry
Database: PDB / ID: 5yvm
TitleCrystal Structure of the archaeal halo-thermophilic Red Sea brine pool alcohol dehydrogenase ADH/D1 bound to NZQ
Componentsalcohol dehydrogenase
KeywordsOXIDOREDUCTASE / protein-cofactor complex / dehydrogenase / NZQ / 5S6S-NADPH(OH)2 / halophilic / thermophilic
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / nucleotide binding / metal ion binding
Similarity search - Function
Iron-type alcohol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 5,6-DIHYDROXY-NADP / Alcohol dehydrogenase iron-type/glycerol dehydrogenase GldA domain-containing protein
Similarity search - Component
Biological speciescandidate divison MSBL1 archaeon SCGC-AAA259E19 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
Model detailsADH/D1 bound to manganese and 5S,6S-NADPH(OH)2 (NZQ)
AuthorsGroetzinger, S.W. / Strillinger, E. / Frank, A. / Eppinger, J. / Groll, M. / Arold, S.T.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
by King Abdullah University of Science and Technology (KAUST)URF/1/1976-06 Saudi Arabia
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Identification and Experimental Characterization of an Extremophilic Brine Pool Alcohol Dehydrogenase from Single Amplified Genomes
Authors: Groetzinger, S.W. / Karan, R. / Strillinger, E. / Bader, S. / Frank, A. / Al Rowaihi, I.S. / Akal, A. / Wackerow, W. / Archer, J.A. / Rueping, M. / Weuster-Botz, D. / Groll, M. / Eppinger, J. / Arold, S.T.
History
DepositionNov 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Experimental preparation ...Database references / Experimental preparation / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / exptl_crystal_grow / struct
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _entity_src_gen.pdbx_gene_src_scientific_name / _exptl_crystal_grow.pdbx_details / _struct.title
Revision 1.2Feb 7, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Nov 22, 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

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Assembly

Deposited unit
A: alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2033
Polymers44,3691
Non-polymers8342
Water1,892105
1
A: alcohol dehydrogenase
hetero molecules

A: alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4076
Polymers88,7382
Non-polymers1,6694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area6320 Å2
ΔGint-29 kcal/mol
Surface area27880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.190, 103.720, 128.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein alcohol dehydrogenase


Mass: 44368.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) candidate divison MSBL1 archaeon SCGC-AAA259E19 (archaea)
Gene: AKJ65_00115 / Plasmid: pTA963 / Production host: Haloferax volcanii (archaea) / Strain (production host): H1895 / References: UniProt: A0A133UP32
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mn
#3: Chemical ChemComp-NZQ / 5,6-DIHYDROXY-NADP


Mass: 779.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C21H32N7O19P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 150mM Mg Acetate, 27% methyl-pentane-diol, 100mM Na cacodylate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97856 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.12→48.092 Å / Num. obs: 21120 / % possible obs: 96 % / Redundancy: 3.6 % / Biso Wilson estimate: 41.74 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.068 / Net I/σ(I): 11.96
Reflection shellResolution: 2.12→2.2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 2104 / CC1/2: 0.84 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALAdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bfj

3bfj


Resolution: 2.12→48.092 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.78
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 625 2.96 %Random selection
Rwork0.1725 ---
obs0.174 21115 95.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.36 Å2 / Biso mean: 56.0437 Å2 / Biso min: 27.56 Å2
Refinement stepCycle: final / Resolution: 2.12→48.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3055 0 51 105 3211
Biso mean--49.75 53.56 -
Num. residues----403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013167
X-RAY DIFFRACTIONf_angle_d1.0484304
X-RAY DIFFRACTIONf_chiral_restr0.057492
X-RAY DIFFRACTIONf_plane_restr0.007553
X-RAY DIFFRACTIONf_dihedral_angle_d18.8021898
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.12-2.33330.27641390.24235121526097
2.3333-2.6710.29561550.21225125528097
2.671-3.3650.27831680.19325126529496
3.365-48.10410.17481630.14445118528193
Refinement TLS params.Method: refined / Origin x: 19.3309 Å / Origin y: 12.4659 Å / Origin z: 46.7351 Å
111213212223313233
T0.3877 Å2-0.0787 Å20.0966 Å2-0.2787 Å2-0.0042 Å2--0.2734 Å2
L2.3958 °20.0343 °2-0.6911 °2-1.5348 °20.0572 °2--3.0303 °2
S0.1847 Å °-0.2278 Å °0.0268 Å °0.322 Å °-0.1395 Å °0.1271 Å °0.0105 Å °-0.1498 Å °-0.0086 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-2 - 400
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allN1
4X-RAY DIFFRACTION1allS1 - 106

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