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- PDB-5yvr: Crystal Structure of the H277A mutant of ADH/D1, an archaeal halo... -

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Basic information

Entry
Database: PDB / ID: 5yvr
TitleCrystal Structure of the H277A mutant of ADH/D1, an archaeal halo-thermophilic Red Sea brine pool alcohol dehydrogenase
Componentsalcohol dehydrogenase
KeywordsOXIDOREDUCTASE / protein-cofactor complex / dehydrogenase / mutant / halophilic / thermophilic
Function / homology
Function and homology information


oxidoreductase activity / 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
: / Chem-NDP / 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 / molecular replacement / Resolution: 1.896 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
King Abdullah University for 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 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity_src_gen / 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 / _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)45,1023
Polymers44,3021
Non-polymers8002
Water1,58588
1
A: alcohol dehydrogenase
hetero molecules

A: alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2046
Polymers88,6042
Non-polymers1,6014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area6190 Å2
ΔGint-33 kcal/mol
Surface area28500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.050, 104.800, 129.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-688-

HOH

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Components

#1: Protein alcohol dehydrogenase /


Mass: 44301.812 Da / Num. of mol.: 1 / Mutation: H277A
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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.896→48.6 Å / Num. obs: 31652 / % possible obs: 99.6 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.031 / Rrim(I) all: 0.062 / Net I/σ(I): 14.9
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 7 % / Rmerge(I) obs: 2.225 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2206 / CC1/2: 0.521 / Rpim(I) all: 1.319 / Rrim(I) all: 2.597 / % possible all: 94.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YVM

5yvm


Resolution: 1.896→33.324 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 28.98
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 2995 9.477 %random selection
Rwork0.179 ---
obs0.1807 31602 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.09 Å2 / Biso mean: 57.8204 Å2 / Biso min: 33.73 Å2
Refinement stepCycle: final / Resolution: 1.896→33.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3050 0 75 88 3213
Biso mean--51.37 49.9 -
Num. residues----403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163159
X-RAY DIFFRACTIONf_angle_d1.284292
X-RAY DIFFRACTIONf_chiral_restr0.07490
X-RAY DIFFRACTIONf_plane_restr0.009554
X-RAY DIFFRACTIONf_dihedral_angle_d18.7431899
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.896-1.9270.57981250.74252469259489
1.927-1.96030.55121460.610527352881100
1.9603-1.99590.50831470.487627512898100
1.9959-2.03430.41121450.369926852830100
2.0343-2.07580.31111450.306727712916100
2.0758-2.12090.26211460.263126822828100
2.1209-2.17030.29121400.243827252865100
2.1703-2.22450.27661450.23827712916100
2.2245-2.28470.26971390.222627352874100
2.2847-2.35190.29141450.19927232868100
2.3519-2.42780.21391410.176627312872100
2.4278-2.51450.23021380.181627422880100
2.5145-2.61510.23191450.18727592904100
2.6151-2.73410.27991440.190427132857100
2.7341-2.87820.27821420.203827422884100
2.8782-3.05840.24111450.204427412886100
3.0584-3.29430.22861450.19227432888100
3.2943-3.62550.21751440.178127582902100
3.6255-4.14930.15691430.143427172860100
4.1493-5.22440.1721440.130727422886100
5.2244-33.32860.16211410.144627542895100
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)
10.7086-0.3228-1.15981.65150.15181.72970.16090.09590.0474-0.0046-0.0409-0.0418-0.29860.2661-0.00080.38-0.00950.07330.4345-0.020.530329.95716.411936.5807
21.8561-0.08540.59072.03740.25422.46490.2731-0.51370.50640.701-0.1654-0.0038-0.64330.1760.00180.7063-0.27310.13550.5956-0.15640.550428.987827.238656.61
30.49780.13690.23620.5941-0.43221.26080.217-0.03440.4740.2731-0.19640.31-0.6657-0.4861-0.00020.6647-0.00090.2330.5734-0.11080.721315.264929.734648.4057
41.150.041-0.39641.86470.14571.97860.3415-0.14990.32120.1937-0.20590.1369-0.5142-0.2764-0.00010.5538-0.05640.16560.4783-0.04370.504918.673622.783145.3197
51.44050.114-1.33141.5887-0.15031.70350.2206-0.2583-0.1270.3474-0.21040.01860.27510.01220.00040.503-0.13380.02410.48340.02030.485424.62876.898747.4644
61.94370.2025-0.77171.8923-0.07212.5990.12-0.1765-0.25850.2262-0.16060.02510.4312-0.1601-0.00070.5259-0.14850.04310.44750.0040.463520.60733.591146.3622
71.1223-0.2853-1.06551.50970.18051.18720.01910.1291-0.4718-0.0015-0.15950.28941.1767-0.47080.00010.8431-0.28540.05120.5646-0.07920.744315.0763-8.010237.8235
81.41060.0446-0.55631.98680.62921.69720.1973-0.17910.0410.4191-0.26310.33750.6011-0.9101-0.00260.6033-0.30440.15990.8197-0.04770.63563.0585.685349.9738
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 28 )A-1 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 98 )A29 - 98
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 131 )A99 - 131
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 182 )A132 - 182
5X-RAY DIFFRACTION5chain 'A' and (resid 183 through 220 )A183 - 220
6X-RAY DIFFRACTION6chain 'A' and (resid 221 through 306 )A221 - 306
7X-RAY DIFFRACTION7chain 'A' and (resid 307 through 349 )A307 - 349
8X-RAY DIFFRACTION8chain 'A' and (resid 350 through 400 )A350 - 400

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