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- PDB-7w9x: Crystal structure of Bacillus subtilis YugJ in complex with nickel -

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Basic information

Entry
Database: PDB / ID: 7w9x
TitleCrystal structure of Bacillus subtilis YugJ in complex with nickel
ComponentsIron-containing alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / aldehyde reductase
Function / homology
Function and homology information


butanol dehydrogenase (NAD+) activity / metal ion binding
Similarity search - Function
Butanol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase
Similarity search - Domain/homology
NICKEL (II) ION / Iron-containing alcohol dehydrogenase
Similarity search - Component
Biological speciesBacillus subtilis subsp. spizizenii ATCC 6633 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å
AuthorsCho, H.Y. / Nam, M.S. / Hong, H.J. / Song, W.S. / Yoon, S.I.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1A2C1002100 Korea, Republic Of
National Research Foundation (NRF, Korea)2019R1I1A1A01047141 Korea, Republic Of
CitationJournal: Int J Mol Sci / Year: 2022
Title: Structural and Biochemical Analysis of the Furan Aldehyde Reductase YugJ from Bacillus subtilis.
Authors: Cho, H.Y. / Nam, M.S. / Hong, H.J. / Song, W.S. / Yoon, S.I.
History
DepositionDec 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Iron-containing alcohol dehydrogenase
B: Iron-containing alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7364
Polymers86,6182
Non-polymers1172
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-34 kcal/mol
Surface area28510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.664, 114.522, 118.736
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 2 and (name N or name...
21(chain B and (resid 2 through 27 or (resid 28...

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
11HISHISHISHIS(chain A and ((resid 2 and (name N or name...AA28
12METMETHOHHOH(chain A and ((resid 2 and (name N or name...AA - E1 - 5027
13METMETHOHHOH(chain A and ((resid 2 and (name N or name...AA - E1 - 5027
14METMETHOHHOH(chain A and ((resid 2 and (name N or name...AA - E1 - 5027
15METMETHOHHOH(chain A and ((resid 2 and (name N or name...AA - E1 - 5027
21HISHISLYSLYS(chain B and (resid 2 through 27 or (resid 28...BB2 - 278 - 33
22SERSERSERSER(chain B and (resid 2 through 27 or (resid 28...BB2834
23METMETHOHHOH(chain B and (resid 2 through 27 or (resid 28...BB - F1 - 5027
24METMETHOHHOH(chain B and (resid 2 through 27 or (resid 28...BB - F1 - 5027
25METMETHOHHOH(chain B and (resid 2 through 27 or (resid 28...BB - F1 - 5027
26METMETHOHHOH(chain B and (resid 2 through 27 or (resid 28...BB - F1 - 5027

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Components

#1: Protein Iron-containing alcohol dehydrogenase


Mass: 43309.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. spizizenii ATCC 6633 (bacteria)
Gene: FAL52_14980 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5F2KLJ3
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 47100 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 32.6
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 5 / Num. unique obs: 2297 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VLJ

1vlj


Resolution: 2.151→29.288 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2407 2376 5.05 %
Rwork0.2032 44658 -
obs0.2051 47034 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.48 Å2 / Biso mean: 48.7395 Å2 / Biso min: 16.67 Å2
Refinement stepCycle: final / Resolution: 2.151→29.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5707 0 2 116 5825
Biso mean--51.13 37.02 -
Num. residues----768
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3163X-RAY DIFFRACTION6.667TORSIONAL
12B3163X-RAY DIFFRACTION6.667TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.151-2.19490.31061480.2512251398
2.1949-2.24260.30111420.24242618100
2.2426-2.29480.26191270.22182597100
2.2948-2.35220.28481250.21612596100
2.3522-2.41570.29951240.22052621100
2.4157-2.48680.26331490.22012590100
2.4868-2.5670.2841380.21652587100
2.567-2.65870.28481470.21172620100
2.6587-2.76510.23991500.21582594100
2.7651-2.89080.25361370.2252633100
2.8908-3.0430.27461570.22952610100
3.043-3.23350.24661260.21712623100
3.2335-3.48280.25431440.21922648100
3.4828-3.83260.2391300.19332674100
3.8326-4.38560.20481220.17812665100
4.3856-5.51930.20331490.17472695100
5.5193-29.2880.20221610.1889277498
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)
12.56580.8833-0.43852.87260.30373.96710.11050.1770.2078-0.27590.1903-0.245-0.91660.5159-0.29330.4303-0.09890.08430.3306-0.07620.265916.889515.1975-43.8051
21.6888-1.088-0.712.4003-0.99146.2823-0.08560.0022-0.2714-0.08120.070.13660.3132-0.05410.01670.1332-0.0312-0.02360.1592-0.02870.288111.4352-6.0566-34.4978
33.63430.0851-0.68762.0788-0.49253.1318-0.2107-0.2089-0.5081-0.02430.0805-0.35070.63850.79560.13140.29720.1653-0.00920.389-0.04070.410627.0387-12.3757-33.7986
40.87910.2548-1.26562.8071-0.79993.73990.2347-0.04070.26770.93710.10310.1671-2.0087-0.0646-0.32171.17620.10330.13370.273-0.02290.32625.876121.4534-11.7313
56.03982.32074.22382.56291.83988.46620.19910.0356-0.33350.33360.09530.1495-0.0269-0.0953-0.33770.19120.03660.01370.17590.04520.28772.8622-1.2352-13.9326
64.80990.03630.69592.50770.44524.42650.087-0.39380.10280.21890.1570.4228-0.157-1.3916-0.18490.28930.07610.04180.64760.10810.3501-12.5522-0.459-14.1766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 184 )A1 - 184
2X-RAY DIFFRACTION2chain 'A' and (resid 185 through 252 )A185 - 252
3X-RAY DIFFRACTION3chain 'A' and (resid 253 through 387 )A253 - 387
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 184 )B1 - 184
5X-RAY DIFFRACTION5chain 'B' and (resid 185 through 248 )B185 - 248
6X-RAY DIFFRACTION6chain 'B' and (resid 249 through 386 )B249 - 386

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