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- PDB-4i5d: Crystal structure of Ralstonia sp. alcohol dehydrogenase in its a... -

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Basic information

Entry
Database: PDB / ID: 4i5d
TitleCrystal structure of Ralstonia sp. alcohol dehydrogenase in its apo form
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
Alclohol dehydrogenase/short-chain dehydrogenase
Similarity search - Component
Biological speciesRalstonia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 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
H: Alclohol dehydrogenase/short-chain dehydrogenase
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,19116
Polymers225,4238
Non-polymers7698
Water8,431468
1
H: Alclohol dehydrogenase/short-chain dehydrogenase
A: Alclohol dehydrogenase/short-chain dehydrogenase
B: Alclohol dehydrogenase/short-chain dehydrogenase
C: Alclohol dehydrogenase/short-chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0968
Polymers112,7114
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13600 Å2
ΔGint-144 kcal/mol
Surface area31780 Å2
MethodPISA
2
D: Alclohol dehydrogenase/short-chain dehydrogenase
E: Alclohol dehydrogenase/short-chain dehydrogenase
F: Alclohol dehydrogenase/short-chain dehydrogenase
G: Alclohol dehydrogenase/short-chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0968
Polymers112,7114
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13620 Å2
ΔGint-143 kcal/mol
Surface area31730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.074, 73.518, 132.677
Angle α, β, γ (deg.)80.610, 86.800, 63.100
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24% PEG3000, 100mM Tris/HCl, 200 mM Li2SO4, 10mM NAD+, pH 8.5, 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: 2.4→30 Å / Num. all: 91854 / Num. obs: 91854 / % possible obs: 96.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 1.993 % / Biso Wilson estimate: 42.351 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 13.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.4-2.50.4142.48211111058296.7
2.5-2.60.3143.2418066905096.8
2.6-2.80.2234.36287541440596.8
2.8-30.1396.66215491080096.7
3-3.50.07511.14349661753597
3.5-40.03620.3119403974096.8
4-60.02428.77278031396096.6
6-80.01834.426680336695.7
8-100.01547.212364119796
100.01349.282367121992.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
XDSdata reduction
PHASERphasing
RefinementStarting model: 4I5E

4i5e


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2026 / WRfactor Rwork: 0.1706 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8292 / SU B: 7.744 / SU ML: 0.172 / SU R Cruickshank DPI: 0.3395 / SU Rfree: 0.2324 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.339 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 4591 5 %RANDOM
Rwork0.1948 87263 --
obs0.1966 91854 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.81 Å2 / Biso mean: 39.4232 Å2 / Biso min: 7.96 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å2-2.01 Å22.51 Å2
2--3.46 Å2-2.61 Å2
3----2.19 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14016 0 40 468 14524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01914224
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.97319280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10451848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34622.74584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.842152368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.52815144
X-RAY DIFFRACTIONr_chiral_restr0.0980.22320
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110560
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A12LOOSE POSITIONAL0.065
12B12LOOSE POSITIONAL0.025
13C12LOOSE POSITIONAL0.025
14D12LOOSE POSITIONAL0.025
15E12LOOSE POSITIONAL0.035
16F12LOOSE POSITIONAL0.035
17G12LOOSE POSITIONAL0.025
18H12LOOSE POSITIONAL0.015
11A1740TIGHT THERMAL6.070.5
12B1740TIGHT THERMAL13.890.5
13C1740TIGHT THERMAL8.010.5
14D1740TIGHT THERMAL7.680.5
15E1740TIGHT THERMAL8.140.5
16F1740TIGHT THERMAL6.620.5
17G1740TIGHT THERMAL6.410.5
18H1740TIGHT THERMAL6.620.5
11A12LOOSE THERMAL5.1710
12B12LOOSE THERMAL17.110
13C12LOOSE THERMAL19.8710
14D12LOOSE THERMAL12.0610
15E12LOOSE THERMAL20.0910
16F12LOOSE THERMAL14.5710
17G12LOOSE THERMAL11.9710
18H12LOOSE THERMAL11.0610
21B12LOOSE POSITIONAL0.025
22C12LOOSE POSITIONAL0.015
23D12LOOSE POSITIONAL0.025
24E12LOOSE POSITIONAL0.035
25F12LOOSE POSITIONAL0.025
26G12LOOSE POSITIONAL0.025
27H12LOOSE POSITIONAL0.015
21B1740TIGHT THERMAL13.430.5
22C1740TIGHT THERMAL7.670.5
23D1740TIGHT THERMAL80.5
24E1740TIGHT THERMAL8.680.5
25F1740TIGHT THERMAL6.270.5
26G1740TIGHT THERMAL6.420.5
27H1740TIGHT THERMAL6.860.5
21B12LOOSE THERMAL17.1710
22C12LOOSE THERMAL19.510
23D12LOOSE THERMAL12.4310
24E12LOOSE THERMAL20.2310
25F12LOOSE THERMAL14.3910
26G12LOOSE THERMAL11.4510
27H12LOOSE THERMAL11.5810
31C12LOOSE POSITIONAL0.015
32D12LOOSE POSITIONAL0.025
33E12LOOSE POSITIONAL0.035
34F12LOOSE POSITIONAL0.025
35G12LOOSE POSITIONAL0.025
36H12LOOSE POSITIONAL0.015
31C1740TIGHT THERMAL8.460.5
32D1740TIGHT THERMAL6.560.5
33E1740TIGHT THERMAL7.140.5
34F1740TIGHT THERMAL7.720.5
35G1740TIGHT THERMAL5.690.5
36H1740TIGHT THERMAL6.160.5
31C12LOOSE THERMAL20.4110
32D12LOOSE THERMAL13.210
33E12LOOSE THERMAL18.1510
34F12LOOSE THERMAL1310
35G12LOOSE THERMAL10.3610
36H12LOOSE THERMAL13.0410
41D12LOOSE POSITIONAL0.025
42E12LOOSE POSITIONAL0.035
43F12LOOSE POSITIONAL0.025
44G12LOOSE POSITIONAL0.025
45H12LOOSE POSITIONAL0.015
41D1740TIGHT THERMAL5.460.5
42E1740TIGHT THERMAL6.20.5
43F1740TIGHT THERMAL8.30.5
44G1740TIGHT THERMAL6.570.5
45H1740TIGHT THERMAL5.420.5
41D12LOOSE THERMAL13.3310
42E12LOOSE THERMAL14.8510
43F12LOOSE THERMAL11.9310
44G12LOOSE THERMAL13.3410
45H12LOOSE THERMAL12.1810
51E12LOOSE POSITIONAL0.035
52F12LOOSE POSITIONAL0.025
53G12LOOSE POSITIONAL0.025
54H12LOOSE POSITIONAL0.015
51E1740TIGHT THERMAL6.410.5
52F1740TIGHT THERMAL7.50.5
53G1740TIGHT THERMAL6.110.5
54H1740TIGHT THERMAL6.140.5
51E12LOOSE THERMAL13.1910
52F12LOOSE THERMAL9.2510
53G12LOOSE THERMAL12.6710
54H12LOOSE THERMAL14.9910
61F12LOOSE POSITIONAL0.015
62G12LOOSE POSITIONAL0.015
63H12LOOSE POSITIONAL0.015
61F1740TIGHT THERMAL6.290.5
62G1740TIGHT THERMAL5.980.5
63H1740TIGHT THERMAL6.490.5
61F12LOOSE THERMAL10.2510
62G12LOOSE THERMAL10.4910
63H12LOOSE THERMAL14.0710
71G12LOOSE POSITIONAL0.015
71G1740TIGHT THERMAL5.390.5
71G12LOOSE THERMAL11.310
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 347 -
Rwork0.297 6489 -
all-6836 -
obs--96.79 %

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