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- PDB-7w9z: Crystal structure of Bacillus subtilis YugJ in complex with NADP ... -

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Basic information

Entry
Database: PDB / ID: 7w9z
TitleCrystal structure of Bacillus subtilis YugJ in complex with NADP and nitrate
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NITRATE ION / Iron-containing alcohol dehydrogenase
Similarity search - Component
Biological speciesBacillus subtilis subsp. spizizenii ATCC 6633 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 / pdbx_initial_refinement_model

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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)88,3538
Polymers86,6182
Non-polymers1,7356
Water10,899605
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-19 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.506, 67.694, 102.374
Angle α, β, γ (deg.)90.000, 100.150, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 20 or (resid 21...
21(chain B and (resid 2 through 23 or (resid 24...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 20 or (resid 21...A2 - 20
121(chain A and (resid 2 through 20 or (resid 21...A21
131(chain A and (resid 2 through 20 or (resid 21...A2 - 504
141(chain A and (resid 2 through 20 or (resid 21...A2 - 504
151(chain A and (resid 2 through 20 or (resid 21...A2 - 504
161(chain A and (resid 2 through 20 or (resid 21...A2 - 504
171(chain A and (resid 2 through 20 or (resid 21...A2 - 504
211(chain B and (resid 2 through 23 or (resid 24...B2 - 23
221(chain B and (resid 2 through 23 or (resid 24...B24
231(chain B and (resid 2 through 23 or (resid 24...B2 - 504
241(chain B and (resid 2 through 23 or (resid 24...B2 - 504
251(chain B and (resid 2 through 23 or (resid 24...B2 - 504
261(chain B and (resid 2 through 23 or (resid 24...B2 - 504

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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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.23 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium nitrate, MES

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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: Jul 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 91189 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 27.4
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 4474 / % possible all: 99

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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: 7W9X

7w9x


Resolution: 1.65→28.914 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1974 4572 5.02 %
Rwork0.1738 86549 -
obs0.175 91121 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.14 Å2 / Biso mean: 22.205 Å2 / Biso min: 7.63 Å2
Refinement stepCycle: final / Resolution: 1.65→28.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5863 0 112 605 6580
Biso mean--15.14 29.65 -
Num. residues----762
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3553X-RAY DIFFRACTION4.68TORSIONAL
12B3553X-RAY DIFFRACTION4.68TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.66880.24411430.2123286299
1.6688-1.68840.24261500.2065283899
1.6884-1.7090.26541620.2084285899
1.709-1.73060.24341430.2066288499
1.7306-1.75340.23021290.2002285099
1.7534-1.77740.21611490.1934288099
1.7774-1.80280.1891610.1812284599
1.8028-1.82970.221610.1823289699
1.8297-1.85830.25691660.18222799100
1.8583-1.88870.21411310.17932889100
1.8887-1.92130.20651610.18122880100
1.9213-1.95620.2221680.17982865100
1.9562-1.99380.21721100.18922897100
1.9938-2.03450.19271610.1752878100
2.0345-2.07880.20381530.17132859100
2.0788-2.12710.19661440.16672925100
2.1271-2.18030.17671640.17052858100
2.1803-2.23920.20491590.17532870100
2.2392-2.30510.22411730.17362866100
2.3051-2.37940.20841480.17242899100
2.3794-2.46440.20971320.17682927100
2.4644-2.5630.18791690.18062893100
2.563-2.67960.20441420.17342903100
2.6796-2.82080.20361550.1792898100
2.8208-2.99730.22271360.18312911100
2.9973-3.22850.19931610.18192904100
3.2285-3.55290.21011560.17512927100
3.5529-4.06580.18111390.15342928100
4.0658-5.11780.13161630.14262933100
5.1178-28.9140.18081830.1742292799
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)
12.1464-2.64690.84975.2227-1.04330.48430.12090.1481-0.0787-0.0194-0.07750.2913-0.0651-0.0564-0.07380.14760.0025-0.00750.1623-0.03250.0667-11.625619.4816-28.3286
21.1425-0.2910.22171.2804-0.07372.10090.01060.02490.03470.01250.01310.1635-0.1053-0.4496-0.02050.08120.0372-0.01690.1943-0.00210.1192-22.342427.3333-17.8517
32.7428-0.6014-1.98931.64650.54516.5332-0.05-0.18190.02070.20410.0912-0.00620.108-0.1506-0.03130.09670.0067-0.02720.15540.00930.1128-17.541419.6295-6.8705
40.5057-0.1727-0.06310.55450.04570.6233-0.0014-0.03810.05710.0215-0.0043-0.07830.03290.0229-0.00540.1153-0.0017-0.01590.12080.00530.1214-0.283418.5089-16.4396
50.96370.66230.12096.8020.00312.2665-0.0098-0.00350.0453-0.17930.0571-0.2933-0.08940.1032-0.05590.03830.0202-0.00910.1002-0.00790.09220.420122.4293-21.0954
61.0806-0.3032-0.41020.9940.24751.3835-0.117-0.1779-0.04860.16410.1198-0.11830.17320.1333-0.01210.19010.0292-0.05450.1433-0.0150.13011.872815.2781-0.5211
75.65120.8486-0.92417.5024-1.26461.8781-0.26220.0361-0.6356-0.27810.30050.1320.1973-0.0642-0.0430.22640.0332-0.03040.15930.02160.1565-4.74629.65747.224
82.31782.0821-0.53613.91720.71720.84950.0431-0.0393-0.00970.1274-0.11150.37560.3127-0.19550.0510.1751-0.040.02370.1621-0.0420.0935-10.634.0535-27.8941
91.94230.5938-0.71031.7234-0.1261.5203-0.01340.0945-0.27790.2586-0.20390.15730.4797-0.50920.19640.2867-0.13860.06560.2652-0.10430.2325-16.5475-11.0916-36.223
101.1538-0.259-0.63981.13940.56851.6990.05820.2176-0.1031-0.1082-0.2590.31480.0563-0.73310.11660.1389-0.014-0.02160.3519-0.10630.1817-18.87250.241-44.1223
111.1606-0.0047-0.19481.3740.68263.88660.07630.1639-0.0515-0.2142-0.16610.0355-0.077-0.38190.0720.12390.0316-0.00830.1982-0.0330.1128-9.91733.3701-50.0563
121.4648-0.4672-0.54011.62920.67831.99960.0501-0.0407-0.14230.0338-0.09930.0630.3017-0.25820.14740.1625-0.04950.02850.1287-0.02710.1225-8.5263-1.9168-32.899
130.83490.4999-0.0483.19840.98821.64570.0050.1183-0.0387-0.2150.0479-0.1036-0.01030.0018-0.05010.11680.01910.01540.13730.00650.1285.0188.2781-39.589
141.0311-0.2345-0.39684.75831.69111.86850.0257-0.0325-0.1950.13450.1155-0.29650.25970.1334-0.12050.09390.0207-0.02260.106-0.00210.15610.5146.4614-31.1237
152.4735-1.1324-0.68967.2501-0.02122.371-0.0692-0.058-0.15570.2880.0169-0.17660.32160.07480.01230.1185-0.0009-0.00910.0969-0.00290.08022.31131.0978-30.3364
165.3521.7596-0.45572.00110.23641.79070.08130.13920.2468-0.34710.0162-0.0972-0.3933-0.0025-0.10910.22160.01250.05710.1135-0.01080.15163.4576.4666-51.3339
170.30920.5112-0.02191.03820.73892.09760.20420.20720.1056-1.12510.569-0.9377-1.34150.932-0.31540.5173-0.14950.32440.3088-0.1340.483918.968117.7654-39.9367
181.68770.2238-0.25851.41310.78612.52840.06960.19970.0727-0.24140.2427-0.2473-0.210.2059-0.26650.1967-0.01120.10140.1561-0.06350.231211.48724.4396-52.7306
194.85010.62672.21563.5783-0.28571.3358-0.41550.0570.51020.30670.20320.2709-0.4561-0.05650.1420.3844-0.01930.11070.16720.00710.24696.818813.6624-58.9416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 28 )A2 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 143 )A29 - 143
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 164 )A144 - 164
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 232 )A165 - 232
5X-RAY DIFFRACTION5chain 'A' and (resid 233 through 261 )A233 - 261
6X-RAY DIFFRACTION6chain 'A' and (resid 262 through 363 )A262 - 363
7X-RAY DIFFRACTION7chain 'A' and (resid 364 through 387 )A364 - 387
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 26 )B2 - 26
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 73 )B27 - 73
10X-RAY DIFFRACTION10chain 'B' and (resid 74 through 143 )B74 - 143
11X-RAY DIFFRACTION11chain 'B' and (resid 144 through 164 )B144 - 164
12X-RAY DIFFRACTION12chain 'B' and (resid 165 through 184 )B165 - 184
13X-RAY DIFFRACTION13chain 'B' and (resid 185 through 210 )B185 - 210
14X-RAY DIFFRACTION14chain 'B' and (resid 211 through 232 )B211 - 232
15X-RAY DIFFRACTION15chain 'B' and (resid 233 through 261 )B233 - 261
16X-RAY DIFFRACTION16chain 'B' and (resid 262 through 296 )B262 - 296
17X-RAY DIFFRACTION17chain 'B' and (resid 297 through 320 )B297 - 320
18X-RAY DIFFRACTION18chain 'B' and (resid 321 through 363 )B321 - 363
19X-RAY DIFFRACTION19chain 'B' and (resid 364 through 387 )B364 - 387

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