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- PDB-4i5e: Crystal structure of Ralstonia sp. alcohol dehydrogenase in compl... -

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Basic information

Entry
Database: PDB / ID: 4i5e
TitleCrystal structure of Ralstonia sp. alcohol dehydrogenase in complex with NADP+
ComponentsAlclohol dehydrogenase/short-chain dehydrogenase
KeywordsOXIDOREDUCTASE / short-chain-dehydrogenases/reductases / Rossmann fold / Ralstonia sp. / alcohol dehydrogenase / RasADH / cosubstrate specificity / NADH / S-phenylethanol
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / nucleotide binding
Similarity search - Function
PKS_KR / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Alclohol dehydrogenase/short-chain dehydrogenase
Similarity search - Component
Biological speciesRalstonia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJarasch, A. / Lerchner, A. / Meining, W. / Schiefner, A. / Skerra, A.
CitationJournal: Biotechnol.Bioeng. / Year: 2013
Title: Crystallographic analysis and structure-guided engineering of NADPH-dependent Ralstonia sp. Alcohol dehydrogenase toward NADH cosubstrate specificity.
Authors: Lerchner, A. / Jarasch, A. / Meining, W. / Schiefner, A. / Skerra, A.
History
DepositionNov 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alclohol dehydrogenase/short-chain dehydrogenase
B: Alclohol dehydrogenase/short-chain dehydrogenase
C: Alclohol dehydrogenase/short-chain dehydrogenase
D: Alclohol dehydrogenase/short-chain dehydrogenase
E: Alclohol dehydrogenase/short-chain dehydrogenase
F: Alclohol dehydrogenase/short-chain dehydrogenase
G: Alclohol dehydrogenase/short-chain dehydrogenase
H: Alclohol dehydrogenase/short-chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,73920
Polymers225,4238
Non-polymers6,31612
Water1,72996
1
A: Alclohol dehydrogenase/short-chain dehydrogenase
B: Alclohol dehydrogenase/short-chain dehydrogenase
C: Alclohol dehydrogenase/short-chain dehydrogenase
D: Alclohol dehydrogenase/short-chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,96111
Polymers112,7114
Non-polymers3,2507
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18840 Å2
ΔGint-97 kcal/mol
Surface area32630 Å2
MethodPISA
2
E: Alclohol dehydrogenase/short-chain dehydrogenase
F: Alclohol dehydrogenase/short-chain dehydrogenase
G: Alclohol dehydrogenase/short-chain dehydrogenase
H: Alclohol dehydrogenase/short-chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,7779
Polymers112,7114
Non-polymers3,0665
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18130 Å2
ΔGint-92 kcal/mol
Surface area32910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.342, 74.549, 132.689
Angle α, β, γ (deg.)80.980, 85.990, 64.600
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
12B
22C
32D
42E
52F
62G
72H
13C
23D
33E
43F
53G
63H
14D
24E
34F
44G
54H
15E
25F
35G
45H
16F
26G
36H
17G
27H

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

#1: Protein
Alclohol dehydrogenase/short-chain dehydrogenase


Mass: 28177.861 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia sp. (bacteria) / Strain: DSMZ 6428 / Gene: RasADH / Plasmid: pASK-IBA35plus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C0IR58
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 26% PEG3000, 100mM Tris/HCl, 200 mM Li2SO4, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 28, 2011
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 57905 / Num. obs: 57905 / % possible obs: 93.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.685 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.8-2.90.5032.1711782593295.4
2.9-30.362.910174512695.4
3-3.50.2064.37349631760394.7
3.5-40.0968.0419177966992.7
4-60.05611.63270891365491.5
6-80.04113.896765343494.6
8-100.03218.052402122895
100.03318.672407125992.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MN0

2mn0


Resolution: 2.8→29.6 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.847 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 19.318 / SU ML: 0.378 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.473 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3052 2942 5.1 %RANDOM
Rwork0.2607 ---
obs0.263 57905 93.71 %-
all-57905 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 191.54 Å2 / Biso mean: 59.7802 Å2 / Biso min: 8.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å21.92 Å20.74 Å2
2--1.33 Å2-3.29 Å2
3----3.21 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15056 0 408 96 15560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01915676
X-RAY DIFFRACTIONr_angle_refined_deg1.4022.00121324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.51651984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21123.293656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.749152576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.60215152
X-RAY DIFFRACTIONr_chiral_restr0.0790.22548
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211584
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A14LOOSE POSITIONAL0.045
12B14LOOSE POSITIONAL0.025
13C14LOOSE POSITIONAL0.015
14D14LOOSE POSITIONAL0.015
15E14LOOSE POSITIONAL0.015
16F14LOOSE POSITIONAL0.025
17G14LOOSE POSITIONAL0.015
18H14LOOSE POSITIONAL0.015
11A1868TIGHT THERMAL9.370.5
12B1868TIGHT THERMAL7.920.5
13C1868TIGHT THERMAL14.270.5
14D1868TIGHT THERMAL9.330.5
15E1868TIGHT THERMAL10.530.5
16F1868TIGHT THERMAL8.750.5
17G1868TIGHT THERMAL10.050.5
18H1868TIGHT THERMAL8.820.5
11A14LOOSE THERMAL13.2710
12B14LOOSE THERMAL14.9410
13C14LOOSE THERMAL20.6210
14D14LOOSE THERMAL9.910
15E14LOOSE THERMAL6.7110
16F14LOOSE THERMAL15.9310
17G14LOOSE THERMAL21.4410
18H14LOOSE THERMAL15.4610
21B14LOOSE POSITIONAL0.025
22C14LOOSE POSITIONAL0.015
23D14LOOSE POSITIONAL0.015
24E14LOOSE POSITIONAL0.015
25F14LOOSE POSITIONAL0.015
26G14LOOSE POSITIONAL0.015
27H14LOOSE POSITIONAL0.015
21B1868TIGHT THERMAL7.610.5
22C1868TIGHT THERMAL13.850.5
23D1868TIGHT THERMAL9.410.5
24E1868TIGHT THERMAL10.810.5
25F1868TIGHT THERMAL8.980.5
26G1868TIGHT THERMAL9.590.5
27H1868TIGHT THERMAL8.910.5
21B14LOOSE THERMAL14.1510
22C14LOOSE THERMAL21.810
23D14LOOSE THERMAL9.2610
24E14LOOSE THERMAL7.8910
25F14LOOSE THERMAL14.510
26G14LOOSE THERMAL20.4410
27H14LOOSE THERMAL16.3510
31C14LOOSE POSITIONAL0.015
32D14LOOSE POSITIONAL0.015
33E14LOOSE POSITIONAL0.015
34F14LOOSE POSITIONAL0.015
35G14LOOSE POSITIONAL0.015
36H14LOOSE POSITIONAL0.015
31C1868TIGHT THERMAL14.060.5
32D1868TIGHT THERMAL9.240.5
33E1868TIGHT THERMAL10.550.5
34F1868TIGHT THERMAL8.80.5
35G1868TIGHT THERMAL9.650.5
36H1868TIGHT THERMAL8.610.5
31C14LOOSE THERMAL22.8710
32D14LOOSE THERMAL10.3310
33E14LOOSE THERMAL7.4810
34F14LOOSE THERMAL14.9210
35G14LOOSE THERMAL19.2410
36H14LOOSE THERMAL14.3810
41D14LOOSE POSITIONAL0.015
42E14LOOSE POSITIONAL0.015
43F14LOOSE POSITIONAL0.015
44G14LOOSE POSITIONAL0.015
45H14LOOSE POSITIONAL0.015
41D1868TIGHT THERMAL8.70.5
42E1868TIGHT THERMAL9.150.5
43F1868TIGHT THERMAL7.820.5
44G1868TIGHT THERMAL11.270.5
45H1868TIGHT THERMAL7.380.5
41D14LOOSE THERMAL11.8910
42E14LOOSE THERMAL10.2610
43F14LOOSE THERMAL12.710
44G14LOOSE THERMAL15.5510
45H14LOOSE THERMAL14.4210
51E14LOOSE POSITIONAL0.015
52F14LOOSE POSITIONAL0.015
53G14LOOSE POSITIONAL0.015
54H14LOOSE POSITIONAL0.015
51E1868TIGHT THERMAL8.520.5
52F1868TIGHT THERMAL7.190.5
53G1868TIGHT THERMAL10.950.5
54H1868TIGHT THERMAL7.960.5
51E14LOOSE THERMAL11.4410
52F14LOOSE THERMAL13.7110
53G14LOOSE THERMAL13.9810
54H14LOOSE THERMAL12.9110
61F14LOOSE POSITIONAL0.015
62G14LOOSE POSITIONAL0.015
63H14LOOSE POSITIONAL0.015
61F1868TIGHT THERMAL7.560.5
62G1868TIGHT THERMAL9.590.5
63H1868TIGHT THERMAL7.840.5
61F14LOOSE THERMAL14.0510
62G14LOOSE THERMAL10.3810
63H14LOOSE THERMAL14.1810
71G14LOOSE POSITIONAL0.015
71G1868TIGHT THERMAL7.90.5
71G14LOOSE THERMAL10.2510
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 244 -
Rwork0.337 4135 -
all-4379 -
obs--95.74 %

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