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- PDB-8uas: Rhodococcus ruber Alcohol Dehydrogenase NADH Biomimetic Complex -... -

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Basic information

Entry
Database: PDB / ID: 8uas
TitleRhodococcus ruber Alcohol Dehydrogenase NADH Biomimetic Complex - Compound 1a
ComponentsRhodococcus ruber Alcohol Dehydrogenase Chain A
KeywordsOXIDOREDUCTASE / Biomimetic / cofactor
Function / homologyCITRIC ACID / ISOPROPYL ALCOHOL / :
Function and homology information
Biological speciesRhodococcus ruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWilson, L.A. / Guddat, L.W. / Schenk, G. / Scott, C.
Funding support Australia, 1items
OrganizationGrant numberCountry
Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australia
CitationJournal: Catalysts / Year: 2024
Title: Structural Characterization of Enzymatic Interactions with Functional Nicotinamide Cofactor Biomimetics
Authors: Rocha, R.A. / Wilson, L.A. / Schwartz, B.D. / Warden, A.C. / Guddat, L.W. / Speight, R.E. / Malins, L. / Schenk, G. / Scott, C.
History
DepositionSep 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhodococcus ruber Alcohol Dehydrogenase Chain A
B: Rhodococcus ruber Alcohol Dehydrogenase Chain A
C: Rhodococcus ruber Alcohol Dehydrogenase Chain A
D: Rhodococcus ruber Alcohol Dehydrogenase Chain A
E: Rhodococcus ruber Alcohol Dehydrogenase Chain A
F: Rhodococcus ruber Alcohol Dehydrogenase Chain A
G: Rhodococcus ruber Alcohol Dehydrogenase Chain A
H: Rhodococcus ruber Alcohol Dehydrogenase Chain A
I: Rhodococcus ruber Alcohol Dehydrogenase Chain A
J: Rhodococcus ruber Alcohol Dehydrogenase Chain A
K: Rhodococcus ruber Alcohol Dehydrogenase Chain A
L: Rhodococcus ruber Alcohol Dehydrogenase Chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)453,93958
Polymers448,71012
Non-polymers5,22946
Water38,3362128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.144, 157.745, 272.429
Angle α, β, γ (deg.)90.00, 91.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Rhodococcus ruber Alcohol Dehydrogenase Chain A


Mass: 37392.473 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus ruber (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 2174 molecules

#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-W3O / 1-[3-[~{tert}-butyl(dimethyl)silyl]oxypropyl]pyridine-3-carboxamide


Mass: 295.473 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C15H27N2O2Si / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2128 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.74 Å3/Da / Density % sol: 67.12 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium Citrate tribasic, pH 5.0, 30% Jeffamine ED

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95373 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.2→49.22 Å / Num. obs: 330537 / % possible obs: 98.9 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.053 / Rrim(I) all: 0.102 / Χ2: 0.55 / Net I/σ(I): 8.9 / Num. measured all: 1170682
Reflection shellResolution: 2.2→2.24 Å / % possible obs: 95.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.75 / Num. measured all: 55999 / Num. unique obs: 15820 / CC1/2: 0.668 / Rpim(I) all: 0.458 / Rrim(I) all: 0.88 / Χ2: 0.53 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.22 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 1995 0.6 %
Rwork0.1821 --
obs0.1823 330393 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30044 0 269 2128 32441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00230977
X-RAY DIFFRACTIONf_angle_d0.50242319
X-RAY DIFFRACTIONf_dihedral_angle_d8.6724607
X-RAY DIFFRACTIONf_chiral_restr0.0454907
X-RAY DIFFRACTIONf_plane_restr0.0035568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.29031400.266422694X-RAY DIFFRACTION96
2.25-2.310.25961450.234323377X-RAY DIFFRACTION99
2.31-2.380.26761430.22623404X-RAY DIFFRACTION99
2.38-2.460.25181390.214923432X-RAY DIFFRACTION99
2.46-2.550.27791460.211823515X-RAY DIFFRACTION99
2.55-2.650.22771380.204923480X-RAY DIFFRACTION99
2.65-2.770.2271480.204123514X-RAY DIFFRACTION99
2.77-2.910.23451450.196123536X-RAY DIFFRACTION99
2.91-3.10.20061340.191923304X-RAY DIFFRACTION98
3.1-3.340.23891410.193923579X-RAY DIFFRACTION99
3.34-3.670.19621490.175123587X-RAY DIFFRACTION99
3.67-4.20.18241390.15623551X-RAY DIFFRACTION99
4.2-5.290.17531420.137423722X-RAY DIFFRACTION99
5.29-49.220.17621460.172523703X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.05720.15360.57590.6430.22240.85990.05930.074-0.2898-0.09670.00220.04530.06830.029-00.2672-0.0119-0.02240.23870.02140.3655-84.8898-29.4612266.9361
20.9430.1823-0.29130.4771-0.10470.3902-0.00390.0713-0.002-0.1105-0.00250.07620.0119-0.0659-00.23810.0045-0.03570.2090.02320.2539-70.5788-11.5613263.7095
31.4506-0.15330.29650.72620.2980.04730.14380.1049-0.0087-0.075-0.15570.15190.0595-0.12660.00020.3077-0.0088-0.07470.2570.04430.2995-85.1527-14.3363263.2254
41.23450.2731-0.21440.60180.42310.440.0913-0.4519-0.0080.1917-0.09290.17010.0574-0.20860.00020.50920.00650.09860.5791-0.08920.4406-55.06094.1294158.0471
51.0095-0.1276-0.02010.6252-0.0540.7165-0.0655-0.09670.09110.1186-0.00520.13-0.0633-0.2298-00.38670.01060.04890.3481-0.07830.3696-46.5346.5567145.4105
61.0596-0.1412-0.29291.41970.15960.31430.0341-0.0893-0.23970.1787-0.0080.1010.22530.0092-00.4553-0.02320.07230.2948-0.040.3261-37.9255-17.5791142.5532
71.18330.1703-0.23720.2180.24530.25350.1201-0.1413-0.18350.0997-0.14760.0988-0.0083-0.158200.4335-0.0780.08310.4326-0.02120.427-56.1064-6.2844146.2918
80.8587-0.4117-0.10361.284-0.97560.9174-0.0494-0.0922-0.2131-0.04210.0961-0.05110.23080.0685-00.48420.0404-0.09410.34240.03430.3213-75.3349.0392235.8936
90.13990.16170.42750.1431-0.55291.21880.01940.0515-0.01790.17450.027-0.12160.17730.009800.38920.0536-0.04050.30910.01130.2632-75.816721.1388226.3123
100.23060.10030.49190.89720.20561.0311-0.09150.1056-0.30840.207-0.12240.41250.4403-0.326-0.00010.4299-0.09270.08860.3933-0.05990.4517-96.050712.334210.6065
110.70040.1072-0.10320.2306-0.23070.9412-0.0041-0.0445-0.2585-0.0136-0.00470.02890.1556-0.1042-00.35730.0087-0.01250.31840.04180.3537-87.078912.904222.7187
121.00790.24160.27892.60460.38640.68380.0235-0.0356-0.00050.05990.0231-0.2192-0.07330.025600.2265-0.0145-0.00620.1860.00810.3387-51.099133.8513273.1049
130.02390.1391-0.3450.7280.1270.1776-0.0205-0.01740.02390.00710.0147-0.0353-0.0390.040700.2411-0.0078-0.03380.17710.01620.3215-56.96517.6867273.847
140.90930.649-0.15281.3492-0.22231.1273-0.0753-0.21380.14560.30930.03590.1793-0.0925-0.165900.31120.05260.0110.2766-0.03590.3445-74.082212.0161287.8998
150.1497-0.148-0.25371.0746-0.56520.1017-0.0247-0.0450.08170.14630.08170.049-0.0236-0.056200.29140.0007-0.02380.2291-0.00310.3761-64.125121.7815278.6636
161.1744-0.2784-0.46780.89190.72321.8349-0.03120.12720.0275-0.09410.0187-0.0081-0.01730.037400.2223-0.0069-0.00820.2934-0.040.2614-22.607455.2784237.8744
170.2271-0.30990.1050.94220.9061.13910.00410.0986-0.0185-0.03720.0034-0.01590.0330.0409-00.2476-0.0201-0.00020.28-0.02320.2714-25.635861.4647250.5321
181.0340.2041-0.3121.260.04361.1204-0.15670.2150.21-0.23130.15880.2789-0.1157-0.2269-00.315-0.016-0.09370.30750.01740.3059-45.395477.993248.7806
190.6151-0.36780.09931.17881.43920.89190.00650.15830.0283-0.1453-0.10980.0876-0.1471-0.07340.00040.27010.001-0.0210.3271-0.01440.2536-35.826266.4967244.1764
200.624-0.5275-0.1560.6490.0820.70770.27520.49360.0661-0.235-0.1476-0.2090.14830.16120.00030.35110.07870.03720.4797-0.01220.4925-26.98643.6449252.168
211.05470.2506-0.72680.2993-0.06580.52840.05590.0583-0.01640.02880.0228-0.14690.00520.082200.18070.0098-0.01910.18980.02580.3544-37.29134.623263.6844
221.4239-0.46610.33331.3903-0.37390.69140.00630.0688-0.0697-0.0643-0.0208-0.09220.0240.08600.24730.00070.01930.20860.01420.2808-44.6965-20.5689266.0978
230.98660.5044-0.02730.53810.1050.36250.18720.1097-0.31140.09740.0032-0.25340.06850.09910.08120.2860.0891-0.070.3107-0.03190.5128-26.1901-6.8475263.6217
240.80040.98060.44361.2941.24231.41420.03280.1693-0.1829-0.04370.089-0.18770.4607-0.03360.00140.43820.0304-0.04020.4615-0.080.2737-85.509113.3448169.9142
250.4340.05540.45130.77340.1681.4648-0.00840.1412-0.0501-0.1520.00620.00260.0373-0.004100.2890.01860.0010.4062-0.05450.233-81.37323.4158183.1469
260.5667-0.07460.02220.6018-0.01590.3486-0.06820.1285-0.34660.110.0134-0.27230.25980.3145-0.00030.40390.1150.01130.5341-0.09880.4804-60.974612.6594194.9477
270.81680.5115-0.08320.3046-0.04550.0548-0.07710.1082-0.35950.03050.057-0.04560.25230.0514-00.44180.0597-0.01320.365-0.07860.3767-75.36299.3795200.0612
280.57760.47720.06630.19250.07281.0730.11440.273-0.3116-0.27890.0252-0.23510.12640.3714-0.01150.39020.1111-0.00740.596-0.15860.3941-71.465618.4028174.4802
291.1216-0.2324-0.54780.3933-0.61131.8262-0.1605-0.25010.00110.1578-0.0464-0.07070.18010.099-0.01290.49860.0120.07020.4290.09570.3092-60.510259.1618174.6303
300.17090.1685-0.48830.4243-0.33171.3755-0.0945-0.0715-0.0365-0.0169-0.00880.01480.233-0.0586-0.00060.46010.02170.07970.38070.09560.3533-60.089662.987159.5772
310.9723-0.1842-0.27381.49240.13911.4656-0.1432-0.28090.12370.31420.1192-0.2945-0.02070.30470.00010.40290.0252-0.03370.41540.03550.29-41.370981.4429159.732
320.6405-0.083-0.70150.8479-0.12870.6078-0.0679-0.3614-0.1001-0.0019-0.0301-0.20160.32750.3865-0.02750.38730.07820.03930.59690.17130.3342-46.520260.5392167.8343
330.51620.3699-0.16510.98780.28641.64770.6511.07890.563-0.1481-0.52860.158-0.4105-0.85650.10810.42050.3597-0.08760.94980.09520.5523-30.453847.811185.5552
340.7252-0.0174-0.28340.57460.50491.12260.06520.14840.0882-0.0605-0.10530.121-0.2055-0.222-0.00110.25690.0533-0.01630.36120.00290.2496-16.225644.5326205.1612
351.11760.2586-0.38130.58250.38680.46070.33040.37640.2848-0.1084-0.37610.4436-0.1293-0.3437-0.0130.31270.10380.0310.5612-0.04250.4811-32.218344.7448200.9911
361.53630.3638-0.51170.67120.42770.94730.1888-0.26980.3330.1413-0.1385-0.1117-0.03470.1832-00.3046-0.0364-0.10040.4735-0.0740.534-52.371444.9976225.3878
371.2240.30850.02390.95330.33240.33140.026-0.06710.0480.19870.0699-0.21670.05060.04610.01690.17630.0127-0.04180.3205-0.00980.2695-62.611438.1711217.5628
380.7468-0.4758-0.27510.7336-0.04921.14680.19030.16250.1873-0.1428-0.0909-0.0634-0.18570.088700.3156-0.01990.0520.38850.0450.2652-66.884548.5843194.2738
391.2004-0.27860.21430.65370.15960.46960.10080.05610.1726-0.08630.0118-0.2555-0.05170.10900.2557-0.02410.0320.3631-0.01140.3272-59.415546.2756207.9448
400.3184-0.06460.3630.82290.06890.37820.1053-0.1368-0.32270.1751-0.0856-0.24270.3060.239500.5490.12040.01120.6040.00160.5731-76.2875-24.7706136.1993
410.7426-0.4129-0.16140.5213-0.22340.4839-0.0057-0.0044-0.0665-0.0749-0.0484-0.10590.18160.1883-00.39880.04170.05030.3833-0.07310.3491-86.5659-15.064129.8321
420.3490.4950.52431.18980.6090.83680.0249-0.1522-0.01040.15720.0373-0.09530.09720.118300.42530.03470.00990.373-0.06810.2881-93.9839-0.7996150.6943
430.5041-0.0202-0.40630.2597-0.03670.61030.2372-0.2065-0.0128-0.0693-0.1426-0.10140.08110.3024-00.4194-0.0346-0.01240.5211-0.0580.4513-75.4001-9.5839139.9981
440.4460.15470.29951.4586-0.45990.3992-0.09090.10640.2013-0.22430.0317-0.0084-0.2415-0.080700.5530.05790.04350.2997-0.00660.4185-36.215537.9124132.0163
450.6272-0.25430.20931.23480.09140.5430.01530.03140.0790.0086-0.02470.0688-0.2597-0.135900.37610.02160.03230.2674-0.03460.3379-34.01122.9167136.0931
461.4043-0.216-0.07440.98490.07990.9569-0.12370.22290.2027-0.25580.1677-0.2362-0.20070.24960.00010.477-0.09590.0680.4001-0.00590.4026-13.560915.9149119.0944
470.5485-0.1564-0.22271.29070.12330.02230.00590.14430.2914-0.18080.0585-0.1683-0.21070.034600.5022-0.01720.04820.36510.01060.4805-23.21625.5125126.9942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -6 through 71 )
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 297 )
3X-RAY DIFFRACTION3chain 'A' and (resid 298 through 345 )
4X-RAY DIFFRACTION4chain 'B' and (resid -3 through 71 )
5X-RAY DIFFRACTION5chain 'B' and (resid 72 through 168 )
6X-RAY DIFFRACTION6chain 'B' and (resid 169 through 297 )
7X-RAY DIFFRACTION7chain 'B' and (resid 298 through 345 )
8X-RAY DIFFRACTION8chain 'C' and (resid -2 through 71 )
9X-RAY DIFFRACTION9chain 'C' and (resid 72 through 168 )
10X-RAY DIFFRACTION10chain 'C' and (resid 169 through 273 )
11X-RAY DIFFRACTION11chain 'C' and (resid 274 through 345 )
12X-RAY DIFFRACTION12chain 'D' and (resid -3 through 82 )
13X-RAY DIFFRACTION13chain 'D' and (resid 83 through 194 )
14X-RAY DIFFRACTION14chain 'D' and (resid 195 through 273 )
15X-RAY DIFFRACTION15chain 'D' and (resid 274 through 345 )
16X-RAY DIFFRACTION16chain 'E' and (resid -2 through 82 )
17X-RAY DIFFRACTION17chain 'E' and (resid 83 through 168 )
18X-RAY DIFFRACTION18chain 'E' and (resid 169 through 273 )
19X-RAY DIFFRACTION19chain 'E' and (resid 274 through 345 )
20X-RAY DIFFRACTION20chain 'F' and (resid -3 through 71 )
21X-RAY DIFFRACTION21chain 'F' and (resid 72 through 168 )
22X-RAY DIFFRACTION22chain 'F' and (resid 169 through 297 )
23X-RAY DIFFRACTION23chain 'F' and (resid 298 through 345 )
24X-RAY DIFFRACTION24chain 'G' and (resid -2 through 71 )
25X-RAY DIFFRACTION25chain 'G' and (resid 72 through 194 )
26X-RAY DIFFRACTION26chain 'G' and (resid 195 through 249 )
27X-RAY DIFFRACTION27chain 'G' and (resid 250 through 297 )
28X-RAY DIFFRACTION28chain 'G' and (resid 298 through 345 )
29X-RAY DIFFRACTION29chain 'H' and (resid -3 through 71 )
30X-RAY DIFFRACTION30chain 'H' and (resid 72 through 168 )
31X-RAY DIFFRACTION31chain 'H' and (resid 169 through 297 )
32X-RAY DIFFRACTION32chain 'H' and (resid 298 through 345 )
33X-RAY DIFFRACTION33chain 'I' and (resid -3 through 82 )
34X-RAY DIFFRACTION34chain 'I' and (resid 83 through 297 )
35X-RAY DIFFRACTION35chain 'I' and (resid 298 through 345 )
36X-RAY DIFFRACTION36chain 'J' and (resid -3 through 82 )
37X-RAY DIFFRACTION37chain 'J' and (resid 83 through 168 )
38X-RAY DIFFRACTION38chain 'J' and (resid 169 through 273 )
39X-RAY DIFFRACTION39chain 'J' and (resid 274 through 345 )
40X-RAY DIFFRACTION40chain 'K' and (resid -4 through 71 )
41X-RAY DIFFRACTION41chain 'K' and (resid 72 through 168 )
42X-RAY DIFFRACTION42chain 'K' and (resid 169 through 297 )
43X-RAY DIFFRACTION43chain 'K' and (resid 298 through 345 )
44X-RAY DIFFRACTION44chain 'L' and (resid -3 through 71 )
45X-RAY DIFFRACTION45chain 'L' and (resid 72 through 168 )
46X-RAY DIFFRACTION46chain 'L' and (resid 169 through 273 )
47X-RAY DIFFRACTION47chain 'L' and (resid 274 through 345 )

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