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- PDB-6z42: The low resolution structure of a zinc-dependent alcohol dehydrog... -

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Basic information

Entry
Database: PDB / ID: 6z42
TitleThe low resolution structure of a zinc-dependent alcohol dehydrogenase from Halomonas elongata.
ComponentsAlcohol dehydrogenase, zinc-containing
KeywordsOXIDOREDUCTASE / Alcohol dehydrogenase / zinc-binding sites
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alcohol dehydrogenase
Similarity search - Component
Biological speciesHalomonas elongata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsGourlay, L.J.
CitationJournal: Chemcatchem / Year: 2020
Title: Uncommon overoxidative catalytic activity in a new halo-tolerant alcohol dehydrogenase
Authors: Contente, M.L. / Fiore, N. / Cannazza, P. / Padrosa, D.R. / Molinari, F. / Gourlay, L.J. / Paradisi, F.
History
DepositionMay 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3May 1, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase, zinc-containing
B: Alcohol dehydrogenase, zinc-containing
C: Alcohol dehydrogenase, zinc-containing
D: Alcohol dehydrogenase, zinc-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,46712
Polymers153,9444
Non-polymers5238
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.662, 104.662, 516.213
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 20 or resid 22...
21(chain B and (resid 6 through 20 or resid 22...
31(chain C and (resid 6 through 23 or (resid 24...
41(chain D and (resid 6 through 20 or resid 22...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLUGLU(chain A and (resid 6 through 20 or resid 22...AA6 - 2027 - 41
12VALVALPROPRO(chain A and (resid 6 through 20 or resid 22...AA22 - 2543 - 46
13PROPROVALVAL(chain A and (resid 6 through 20 or resid 22...AA27 - 5548 - 76
14LYSLYSLYSLYS(chain A and (resid 6 through 20 or resid 22...AA5677
15ASPASPALAALA(chain A and (resid 6 through 20 or resid 22...AA2 - 34123 - 362
16ASPASPALAALA(chain A and (resid 6 through 20 or resid 22...AA2 - 34123 - 362
17ASPASPALAALA(chain A and (resid 6 through 20 or resid 22...AA2 - 34123 - 362
18ASPASPALAALA(chain A and (resid 6 through 20 or resid 22...AA2 - 34123 - 362
21LYSLYSGLUGLU(chain B and (resid 6 through 20 or resid 22...BB6 - 2027 - 41
22VALVALPROPRO(chain B and (resid 6 through 20 or resid 22...BB22 - 2343 - 44
23THRTHRALAALA(chain B and (resid 6 through 20 or resid 22...BB4 - 34125 - 362
24THRTHRALAALA(chain B and (resid 6 through 20 or resid 22...BB4 - 34125 - 362
25THRTHRALAALA(chain B and (resid 6 through 20 or resid 22...BB4 - 34125 - 362
26THRTHRALAALA(chain B and (resid 6 through 20 or resid 22...BB4 - 34125 - 362
27THRTHRALAALA(chain B and (resid 6 through 20 or resid 22...BB4 - 34125 - 362
28THRTHRALAALA(chain B and (resid 6 through 20 or resid 22...BB4 - 34125 - 362
31LYSLYSPROPRO(chain C and (resid 6 through 23 or (resid 24...CC6 - 2327 - 44
32VALVALVALVAL(chain C and (resid 6 through 23 or (resid 24...CC2445
33LYSLYSILEILE(chain C and (resid 6 through 23 or (resid 24...CC6 - 33227 - 353
34LYSLYSILEILE(chain C and (resid 6 through 23 or (resid 24...CC6 - 33227 - 353
35LYSLYSILEILE(chain C and (resid 6 through 23 or (resid 24...CC6 - 33227 - 353
36LYSLYSILEILE(chain C and (resid 6 through 23 or (resid 24...CC6 - 33227 - 353
41LYSLYSGLUGLU(chain D and (resid 6 through 20 or resid 22...DD6 - 2027 - 41
42VALVALPROPRO(chain D and (resid 6 through 20 or resid 22...DD22 - 2343 - 44
43VALVALVALVAL(chain D and (resid 6 through 20 or resid 22...DD2445
44METMETALAALA(chain D and (resid 6 through 20 or resid 22...DD5 - 34126 - 362
45METMETALAALA(chain D and (resid 6 through 20 or resid 22...DD5 - 34126 - 362
46METMETALAALA(chain D and (resid 6 through 20 or resid 22...DD5 - 34126 - 362
47METMETALAALA(chain D and (resid 6 through 20 or resid 22...DD5 - 34126 - 362

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.689355, 0.724334, 0.01136), (0.724276, 0.688814, 0.030982), (0.014616, 0.029585, -0.999455)-1.64671, -0.24731, 44.1786
3given(1), (1), (1)
4given(0.649173, -0.71572, 0.257524), (-0.714203, -0.690028, -0.117367), (0.261701, -0.107733, -0.959117)29.39563, 84.468071, 44.613541
5given(1), (1), (1)
6given(-0.959374, -0.008409, -0.282012), (-0.013986, -0.996909, 0.077306), (-0.281791, 0.07811, 0.956291)40.118519, 80.932411, 2.5842
7given(1), (1), (1)
8given(-0.961531, -0.009414, -0.274536), (-0.012492, -0.99688, 0.077937), (-0.274413, 0.078368, 0.958413)40.011379, 80.829437, 2.512
9given(1), (1), (1)
10given(0.647116, -0.714937, 0.264775), (-0.712702, -0.690614, -0.122914), (0.270734, -0.109166, -0.956445)29.377069, 84.941994, 44.542889
11given(1), (1), (1)
12given(-0.686254, 0.727264, 0.011921), (0.726937, 0.685202, 0.045394), (0.024845, 0.039818, -0.998898)-1.53477, -0.69663, 43.49144

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Components

#1: Protein
Alcohol dehydrogenase, zinc-containing


Mass: 38485.898 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halomonas elongata (strain ATCC 33173 / DSM 2581 / NBRC 15536 / NCIMB 2198 / 1H9) (bacteria)
Gene: adh2, HELO_2818 / Plasmid: pET-28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLYsS / References: UniProt: E1V3M3, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: B8 PACT SCREEN (Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→48.54 Å / Num. obs: 15280 / % possible obs: 99.9 % / Redundancy: 30.9 % / CC1/2: 0.994 / Rpim(I) all: 0.15 / Χ2: 1.01 / Net I/σ(I): 9.6
Reflection shellResolution: 4→4.47 Å / Redundancy: 32.9 % / Rmerge(I) obs: 3.99 / Num. unique obs: 4182 / CC1/2: 0.643 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BALBES MODEL

Resolution: 4→48.496 Å / SU ML: 0.73 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3671 1516 10 %RANDOM
Rwork0.3287 13647 --
obs0.3326 15163 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 274.58 Å2 / Biso mean: 115.9548 Å2 / Biso min: 56.28 Å2
Refinement stepCycle: final / Resolution: 4→48.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9725 0 8 0 9733
Biso mean--95.99 --
Num. residues----1318
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5423X-RAY DIFFRACTION13.899TORSIONAL
12B5423X-RAY DIFFRACTION13.899TORSIONAL
13C5423X-RAY DIFFRACTION13.899TORSIONAL
14D5423X-RAY DIFFRACTION13.899TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
4.0003-4.12940.42011330.42151196
4.1294-4.27690.35471320.38941192
4.2769-4.4480.35431350.36211206
4.448-4.65030.41961340.3511208
4.6503-4.89520.35231340.33831214
4.8952-5.20160.37141340.35541216
5.2016-5.60270.42681360.34411217
5.6027-6.16550.41671400.36141258
6.1655-7.05530.35271380.35231242
7.0553-8.88010.32991440.29481289
8.8801-48.4960.35581560.28331409
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)
10.39340.1617-0.09040.353-0.0682-0.003-0.24460.0747-1.11080.9493-0.8063-0.2729-0.1189-1.8012-0.06581.73660.01940.46741.237-0.49361.2864-3.056233.201749.6535
20.06260.1534-0.0030.5664-0.23260.1912-0.08790.4672-0.74330.6573-0.27870.47670.3732-0.9403-0.09010.76830.31050.43031.1719-0.75721.0166-5.090136.284927.9631
30.2124-0.07290.13660.06250.11810.5351-0.0780.4296-0.2033-0.0108-0.3960.54140.23640.00560.0110.86510.52450.2560.4742-0.68210.78573.145825.237219.8341
40.21130.11120.23920.07380.15930.2615-0.08350.15170.1437-0.02310.26170.2284-0.64750.14260.10070.9082-0.02730.43080.1341-0.19071.3979-7.063543.631734.888
50.20280.03590.05210.0179-0.01070.0620.2263-0.213-0.15830.00350.14880.2704-0.1414-0.06830.03932.2093-0.27290.4910.6206-0.00621.6663-18.648228.320340.8552
60.3874-0.0126-0.3640.2127-0.06530.34260.5606-0.01770.11190.0007-0.25930.5879-0.0283-0.26010.2021.638-0.2029-0.07631.1038-1.12071.497726.650312.5741-11.3111
70.2524-0.3478-0.01520.4793-0.08040.2588-0.33020.8941-0.4478-0.11440.13030.5898-0.69990.16350.02840.7074-0.4951-0.28210.9682-0.89490.719723.977624.9334-1.7974
80.3346-0.0564-0.09320.54740.07110.04520.50820.3396-0.0483-0.01560.1125-0.4999-0.12150.66140.95581.08830.2769-0.15260.1359-0.64750.307630.993124.095916.2855
90.06020.00670.03140.0272-0.02780.0258-0.32180.2491-0.44190.273-0.09630.53370.03440.42-0.00061.39410.0518-0.4910.8639-0.42921.332625.644214.089335.5227
100.21660.03640.1171-0.01-0.02540.2286-0.11110.3676-0.8064-0.06180.1635-0.04320.5790.5689-0.00010.6463-0.21490.18220.7925-0.35860.982118.257822.712922.3946
110.0060.0229-0.03020.0389-0.07360.15240.1311-0.17190.01040.1839-0.0086-0.0792-0.1576-0.29960.17290.8159-0.26160.21631.6244-1.29350.984834.180210.23386.6605
120.11930.0884-0.05250.0823-0.0090.0664-0.59960.0203-0.1299-0.3218-0.24750.07310.53230.0039-0.00562.4451-0.50580.40832.80150.46391.40618.342266.5139-14.3396
130.2379-0.1115-0.04880.1471-0.0080.1488-0.7735-0.37850.265-0.1798-0.6133-0.55960.0119-0.4537-0.00592.19770.356-0.04451.42980.18941.202314.657758.1129-6.8183
140.4182-0.2191-0.12160.11440.06620.18750.36371.19320.51530.0749-0.59180.62650.1534-0.3695-0.02051.3548-0.17340.02261.5122-0.16331.123113.797253.16323.9454
150.0221-0.02470.00870.0185-0.00930.0225-0.08960.36660.0909-0.0606-0.2877-0.1714-0.0879-0.0890.00042.18080.6280.4571.5004-0.29531.36221.209862.593617.4185
160.03690.01520.07620.05820.11080.1446-0.31780.14260.41280.22750.27270.5028-1.4453-0.1715-0.00031.6550.1948-0.10030.8238-0.24051.23315.298264.053925.5713
170.15740.007-0.2050.25-0.45851.0176-0.01530.4981-0.1865-0.09640.45350.3987-0.82240.21820.03880.9116-0.17550.07921.9892-0.75221.51156.198364.31112.134
180.3358-0.17250.02220.16580.11250.33090.4687-0.00090.66710.4861-0.29081.1922-0.079-0.72420.012.2963-0.41670.19661.1964-0.36251.422831.621252.658355.9678
190.67530.1705-0.21020.24910.01010.07080.5103-0.432-0.30460.03270.1073-0.2315-0.00670.4018-0.07191.4492-0.72430.41770.647-1.05591.401825.62346.827247.767
200.0959-0.1020.00380.2867-0.19520.1972-0.4351-0.34540.50860.44970.1019-0.4095-0.088-0.0927-0.03920.9606-0.22050.13141.1193-0.37260.901540.724947.155825.008
211.0683-0.35130.17030.6333-0.29070.33580.42940.35960.7173-0.48590.0178-0.632-0.62970.79121.35940.41120.05290.93660.7613-1.0670.902633.734952.164829.7134
220.47750.1257-0.11690.29980.14160.13410.287-0.11050.09970.0265-0.0539-0.3103-0.0598-0.06870.38032.3262-0.2883-0.22031.4031-1.02540.954446.079356.014547.4862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 109 )A2 - 109
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 231 )A110 - 231
3X-RAY DIFFRACTION3chain 'A' and (resid 232 through 292 )A232 - 292
4X-RAY DIFFRACTION4chain 'A' and (resid 293 through 316 )A293 - 316
5X-RAY DIFFRACTION5chain 'A' and (resid 317 through 341 )A317 - 341
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 30 )B4 - 30
7X-RAY DIFFRACTION7chain 'B' and (resid 31 through 126 )B31 - 126
8X-RAY DIFFRACTION8chain 'B' and (resid 127 through 211 )B127 - 211
9X-RAY DIFFRACTION9chain 'B' and (resid 212 through 231 )B212 - 231
10X-RAY DIFFRACTION10chain 'B' and (resid 232 through 305 )B232 - 305
11X-RAY DIFFRACTION11chain 'B' and (resid 306 through 341 )B306 - 341
12X-RAY DIFFRACTION12chain 'C' and (resid 6 through 30 )C6 - 30
13X-RAY DIFFRACTION13chain 'C' and (resid 31 through 85 )C31 - 85
14X-RAY DIFFRACTION14chain 'C' and (resid 86 through 178 )C86 - 178
15X-RAY DIFFRACTION15chain 'C' and (resid 179 through 211 )C179 - 211
16X-RAY DIFFRACTION16chain 'C' and (resid 212 through 292 )C212 - 292
17X-RAY DIFFRACTION17chain 'C' and (resid 293 through 332 )C293 - 332
18X-RAY DIFFRACTION18chain 'D' and (resid 5 through 85 )D5 - 85
19X-RAY DIFFRACTION19chain 'D' and (resid 86 through 152 )D86 - 152
20X-RAY DIFFRACTION20chain 'D' and (resid 153 through 231 )D153 - 231
21X-RAY DIFFRACTION21chain 'D' and (resid 232 through 320 )D232 - 320
22X-RAY DIFFRACTION22chain 'D' and (resid 321 through 341 )D321 - 341

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