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- PDB-7w9y: Crystal structure of Bacillus subtilis YugJ in complex with NADP ... -

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Basic information

Entry
Database: PDB / ID: 7w9y
TitleCrystal structure of Bacillus subtilis YugJ in complex with NADP and 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 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: 1.93 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

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Assembly

Deposited unit
A: Iron-containing alcohol dehydrogenase
B: Iron-containing alcohol dehydrogenase
C: Iron-containing alcohol dehydrogenase
D: Iron-containing alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,44512
Polymers173,2374
Non-polymers3,2088
Water14,268792
1
A: Iron-containing alcohol dehydrogenase
B: Iron-containing alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2236
Polymers86,6182
Non-polymers1,6044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-42 kcal/mol
Surface area26780 Å2
MethodPISA
2
C: Iron-containing alcohol dehydrogenase
D: Iron-containing alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2236
Polymers86,6182
Non-polymers1,6044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-42 kcal/mol
Surface area26770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.036, 69.641, 87.609
Angle α, β, γ (deg.)96.290, 91.030, 90.370
Int Tables number1
Space group name H-MP1
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 26 or (resid 27...
31(chain C and ((resid 2 and (name N or name...
41(chain D and (resid 2 through 23 or (resid 24...

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
12ASPASPNINI(chain A and ((resid 2 and (name N or name...AA - F-1 - 5025
13ASPASPNINI(chain A and ((resid 2 and (name N or name...AA - F-1 - 5025
14ASPASPNINI(chain A and ((resid 2 and (name N or name...AA - F-1 - 5025
15ASPASPNINI(chain A and ((resid 2 and (name N or name...AA - F-1 - 5025
21HISHISLEULEU(chain B and (resid 2 through 26 or (resid 27...BB2 - 268 - 32
22LYSLYSLYSLYS(chain B and (resid 2 through 26 or (resid 27...BB2733
23HISHISNINI(chain B and (resid 2 through 26 or (resid 27...BB - H2 - 5028
24HISHISNINI(chain B and (resid 2 through 26 or (resid 27...BB - H2 - 5028
25HISHISNINI(chain B and (resid 2 through 26 or (resid 27...BB - H2 - 5028
31HISHISHISHIS(chain C and ((resid 2 and (name N or name...CC28
32ASPASPNINI(chain C and ((resid 2 and (name N or name...CC - J-1 - 5025
33ASPASPNINI(chain C and ((resid 2 and (name N or name...CC - J-1 - 5025
34ASPASPNINI(chain C and ((resid 2 and (name N or name...CC - J-1 - 5025
35ASPASPNINI(chain C and ((resid 2 and (name N or name...CC - J-1 - 5025
41HISHISPROPRO(chain D and (resid 2 through 23 or (resid 24...DD2 - 238 - 29
42GLUGLUGLUGLU(chain D and (resid 2 through 23 or (resid 24...DD2430
43HISHISNINI(chain D and (resid 2 through 23 or (resid 24...DD - L2 - 5028
44HISHISNINI(chain D and (resid 2 through 23 or (resid 24...DD - L2 - 5028
45HISHISNINI(chain D and (resid 2 through 23 or (resid 24...DD - L2 - 5028
46HISHISNINI(chain D and (resid 2 through 23 or (resid 24...DD - L2 - 5028

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Components

#1: Protein
Iron-containing alcohol dehydrogenase


Mass: 43309.172 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 792 / 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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, calcium acetate, 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: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.93→30 Å / Num. obs: 112718 / % possible obs: 96.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 19.1
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 5537 / % possible all: 95.3

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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: 1.93→29.848 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 21.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 5775 5.13 %
Rwork0.1701 106897 -
obs0.172 112672 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.45 Å2 / Biso mean: 29.3382 Å2 / Biso min: 9.77 Å2
Refinement stepCycle: final / Resolution: 1.93→29.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11833 0 164 792 12789
Biso mean--22.86 32.45 -
Num. residues----1549
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6989X-RAY DIFFRACTION5.382TORSIONAL
12B6989X-RAY DIFFRACTION5.382TORSIONAL
13C6989X-RAY DIFFRACTION5.382TORSIONAL
14D6989X-RAY DIFFRACTION5.382TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.93-1.95190.27431760.2376340392
1.9519-1.97490.24541690.2271351396
1.9749-1.9990.29341910.2239361696
1.999-2.02430.24591900.216347496
2.0243-2.05090.25152010.2123357496
2.0509-2.0790.24482010.2045350496
2.079-2.10870.26342120.1942352396
2.1087-2.14010.2542340.192353196
2.1401-2.17360.24791740.1898358397
2.1736-2.20920.24171960.1811353896
2.2092-2.24730.21441920.1724358797
2.2473-2.28810.19962240.1712349097
2.2881-2.33210.21192270.1668355097
2.3321-2.37970.20762020.1693352797
2.3797-2.43140.21181850.1657358697
2.4314-2.4880.22061820.174357497
2.488-2.55020.21171630.168361897
2.5502-2.61910.20821810.1645360797
2.6191-2.69610.2112110.1683356697
2.6961-2.7830.2071900.1727359997
2.783-2.88240.19282210.1637355097
2.8824-2.99770.22141910.1754362098
2.9977-3.1340.22491400.1773366398
3.134-3.29910.19761230.1786368097
3.2991-3.50550.21541880.1738357097
3.5055-3.77560.19742470.1625353698
3.7756-4.15470.17812140.1425359798
4.1547-4.75380.15632370.1374356598
4.7538-5.98140.2011650.1582363097
5.9814-29.8480.18611480.1611352395
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)
11.6512-0.88830.34952.40020.21611.13040.10380.19830.1041-0.593-0.0909-0.07920.0407-0.0071-0.06220.22150.00020.00520.1503-0.00050.0803-19.33831.2494-15.0679
21.7555-0.1184-0.08182.6615-0.34631.410.0750.08350.1759-0.4037-0.0550.2835-0.1416-0.1903-0.02620.19250.0353-0.05480.13580.0160.1386-29.016439.948-11.8887
30.4434-0.1682-0.31586.0237-0.43750.75440.0632-0.1221-0.0148-0.0036-0.13910.00470.00690.07460.05320.0864-0.0475-0.0430.20550.00690.1127-14.754829.78137.0131
48.01861.64580.50365.88160.93394.29710.2113-0.074-0.1070.0473-0.1661-0.7973-0.33640.242-0.06950.1263-0.0402-0.01070.15260.03880.1396-8.84639.1375-1.856
52.3858-0.83080.74462.6606-0.34521.69480.0656-0.3418-0.05440.1994-0.00040.09850.0199-0.2199-0.0650.1363-0.07370.01880.254-0.00240.1272-22.201429.226413.1421
62.9869-0.0240.54661.8976-0.58831.23970.0212-0.62310.15690.44860.09090.3293-0.2012-0.4505-0.10430.2013-0.01950.07870.4076-0.04910.1823-28.325835.182817.1901
71.38780.08890.45823.4286-0.43551.5629-0.11860.3558-0.3577-0.9196-0.0317-0.71760.32-0.07650.14440.3766-0.02810.21360.1821-0.08190.366-14.19945.7934-20.0326
83.18190.2668-0.23024.72520.90880.59070.0319-0.1215-0.0821-0.172-0.09450.0810.08470.0710.05080.1353-0.0256-0.02630.21150.08160.1325-4.176612.5303-0.5584
92.08970.3534-0.30192.8198-1.25032.328-0.07420.22480.0295-0.766-0.3076-0.64750.3980.3040.20980.34160.0560.13820.29880.13810.337810.553913.9143-6.9189
101.12070.40880.03033.60510.41391.18280.0039-0.1037-0.04120.36540.09350.0609-0.01010.0504-0.14820.17850.0239-0.04140.13860.02710.111218.74575.9105-44.5744
111.7264-0.1298-0.21782.30780.10891.5419-0.0392-0.05340.09040.26250.1049-0.424-0.13570.294-0.0630.1833-0.0243-0.08590.1544-0.02780.187828.324114.6361-47.7105
120.16790.1026-0.14065.66271.04281.6724-0.06760.05920.0374-0.04150.01750.0226-0.1412-0.01810.05330.0813-0.0016-0.05450.15980.0130.130912.47887.5827-64.269
132.61681.1720.59242.85850.6122.3863-0.00970.2623-0.1007-0.32980.1031-0.2234-0.06650.3547-0.08120.13980.01540.02760.2088-0.00310.174421.95594.0194-72.881
143.1618-0.22150.70525.65783.00953.31650.07910.4021-0.0013-0.979-0.1068-0.2475-0.44760.0120.06240.29380.01340.0020.20970.05930.146414.59357.7384-80.0982
152.1249-0.19050.23481.22191.1281.1735-0.26130.690.0999-0.85940.6393-0.8217-0.75670.9705-0.22390.1866-0.22020.18620.6193-0.13010.400633.601911.0718-75.5733
161.9211-0.32490.0752.7740.33251.3634-0.0749-0.3329-0.09480.68280.1159-0.0670.1657-0.0417-0.03460.31610.0432-0.07090.19310.03350.092513.6652-19.7432-39.8607
172.0337-0.7685-0.06193.5256-0.49440.53920.0941-0.00620.08890.0551-0.09090.02710.0225-0.02850.00990.1079-0.0092-0.03520.179-0.01720.06723.9196-12.7741-59.5689
181.9508-0.5233-0.28322.5081-0.13952.107-0.0277-0.1805-0.04470.3155-0.05740.42560.0083-0.36870.03350.158-0.0320.03130.3045-0.05660.2177-11.0358-12.0754-52.7604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 37 )A-1 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 184 )A38 - 184
3X-RAY DIFFRACTION3chain 'A' and (resid 185 through 232 )A185 - 232
4X-RAY DIFFRACTION4chain 'A' and (resid 233 through 252 )A233 - 252
5X-RAY DIFFRACTION5chain 'A' and (resid 253 through 320 )A253 - 320
6X-RAY DIFFRACTION6chain 'A' and (resid 321 through 387 )A321 - 387
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 184 )B2 - 184
8X-RAY DIFFRACTION8chain 'B' and (resid 185 through 252 )B185 - 252
9X-RAY DIFFRACTION9chain 'B' and (resid 253 through 387 )B253 - 387
10X-RAY DIFFRACTION10chain 'C' and (resid -1 through 37 )C-1 - 37
11X-RAY DIFFRACTION11chain 'C' and (resid 38 through 184 )C38 - 184
12X-RAY DIFFRACTION12chain 'C' and (resid 185 through 252 )C185 - 252
13X-RAY DIFFRACTION13chain 'C' and (resid 253 through 320 )C253 - 320
14X-RAY DIFFRACTION14chain 'C' and (resid 321 through 339 )C321 - 339
15X-RAY DIFFRACTION15chain 'C' and (resid 340 through 387 )C340 - 387
16X-RAY DIFFRACTION16chain 'D' and (resid 2 through 184 )D2 - 184
17X-RAY DIFFRACTION17chain 'D' and (resid 185 through 252 )D185 - 252
18X-RAY DIFFRACTION18chain 'D' and (resid 253 through 387 )D253 - 387

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