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- PDB-1llu: THE TERNARY COMPLEX OF PSEUDOMONAS AERUGINOSA ALCOHOL DEHYDROGENA... -

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Basic information

Entry
Database: PDB / ID: 1llu
TitleTHE TERNARY COMPLEX OF PSEUDOMONAS AERUGINOSA ALCOHOL DEHYDROGENASE WITH ITS COENZYME AND WEAK SUBSTRATE
ComponentsAlcohol Dehydrogenase
KeywordsOXIDOREDUCTASE / Enzyme-coenzyme-substrate complex / proton relay system / NADH / Alcohol Dehydrogenase
Function / homology
Function and homology information


alcohol dehydrogenase / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / alcohol dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLevin, I. / Meiri, G. / Peretz, M. / Frolow, F. / Burstein, Y.
CitationJournal: Protein Sci. / Year: 2004
Title: The ternary complex of Pseudomonas aeruginosa alcohol dehydrogenase with NADH and ethylene glycol.
Authors: Levin, I. / Meiri, G. / Peretz, M. / Burstein, Y. / Frolow, F.
History
DepositionApr 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Author states residue ALA 229 and ILE 230 were verified by DNA sequencing, there are two ...SEQUENCE Author states residue ALA 229 and ILE 230 were verified by DNA sequencing, there are two conflicts between the strain Habs serotype I used in this study (Kessler, E., Safrin, M., Peretz, M., and Burstein, Y. (1992). Identification of cleavage sites involved in proteolytic processing of Pseudomonas aeruginosa preproelastase, FEBS Lett 299, 291-3) and the sequence in data base.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol Dehydrogenase
B: Alcohol Dehydrogenase
C: Alcohol Dehydrogenase
D: Alcohol Dehydrogenase
E: Alcohol Dehydrogenase
F: Alcohol Dehydrogenase
G: Alcohol Dehydrogenase
H: Alcohol Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,45244
Polymers287,3538
Non-polymers7,09936
Water18,8081044
1
A: Alcohol Dehydrogenase
B: Alcohol Dehydrogenase
C: Alcohol Dehydrogenase
D: Alcohol Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,22622
Polymers143,6774
Non-polymers3,54918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16520 Å2
ΔGint-235 kcal/mol
Surface area45690 Å2
MethodPISA
2
E: Alcohol Dehydrogenase
F: Alcohol Dehydrogenase
G: Alcohol Dehydrogenase
H: Alcohol Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,22622
Polymers143,6774
Non-polymers3,54918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16520 Å2
ΔGint-236 kcal/mol
Surface area45690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.171, 86.328, 125.698
Angle α, β, γ (deg.)79.34, 78.66, 71.58
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.72417, -0.09256, -0.68339), (-0.09185, -0.96918, 0.22859), (-0.68348, 0.22831, 0.69335)82.48212, 18.86833, -11.46263
DetailsCoordinates for biologically active tetramer are provided. The second tetramer in assymetric unit can be generated by rotation: (-0.72417 -0.09256 -0.68339 ), ( -0.09185 -0.96918 0.22859 ), (-0.68348 0.22831 0.69335 ) and translation (in A) (82.48212 18.86833 -11.46263)

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Components

#1: Protein
Alcohol Dehydrogenase / Aldehyde reductase


Mass: 35919.180 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: Habs serotype I / Gene: adh / Plasmid: BS-p80 / Production host: Escherichia coli (E. coli) / Strain (production host): TG-I / References: UniProt: Q9HTD9, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1044 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 2mM NAD+, 16mM Spermine, 14% Polyethelene Glycol Monomethyl Ether 2000, 12mM Sodium Potassium Tartrate, 100mM Tris pH 8.6, 0.1mM DTT, 0.007% Sodium Azide, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K
Crystal grow
*PLUS
Temperature: 19 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 %PEG2000 MME1reservoir
212 mMsodium potassium tartrate1reservoir
3100 mMTris1reservoir
40.1 mMdithiothreitol1reservoir
50.007 %sodium azide1reservoirpH8.6
63.8 mg/mlprotein1drop
72 mMNAD+1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 27, 2001 / Details: Osmic-Blue confocal optics
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 123136 / Num. obs: 123136 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.108 / Net I/σ(I): 12.1
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 6019 / Rsym value: 0.463 / % possible all: 94.2
Reflection
*PLUS
Highest resolution: 2.3 Å / Rmerge(I) obs: 0.108
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 94.2 % / Rmerge(I) obs: 0.463

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
MOLREPphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YKF

1ykf


Resolution: 2.3→19.99 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1547341.28 / Data cutoff high rms absF: 1547341.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 12264 10 %RANDOM
Rwork0.229 ---
all-123136 --
obs-123017 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.711 Å2 / ksol: 0.363236 e/Å3
Displacement parametersBiso mean: 31.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.49 Å2-4.99 Å20.21 Å2
2---0.85 Å22.01 Å2
3----3.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20120 0 416 1044 21580
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.19
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.942
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.942.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.307 1200 10 %
Rwork0.299 10800 -
obs--94.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4NAD_EGL_EDO_XPLOR_PAR.TXTNAD_EGL_EDO_XPLOR_TOP.TXT
Refinement
*PLUS
Highest resolution: 2.3 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.18

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