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- PDB-1flg: CRYSTAL STRUCTURE OF THE QUINOPROTEIN ETHANOL DEHYDROGENASE FROM ... -

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Basic information

Entry
Database: PDB / ID: 1flg
TitleCRYSTAL STRUCTURE OF THE QUINOPROTEIN ETHANOL DEHYDROGENASE FROM PSEUDOMONAS AERUGINOSA
ComponentsPROTEIN (QUINOPROTEIN ETHANOL DEHYDROGENASE)
KeywordsOXIDOREDUCTASE / QUINOPROTEIN / SUPERBARREL / DEHYDROGENASE
Function / homology
Function and homology information


alcohol dehydrogenase (cytochrome c) / alcohol dehydrogenase (cytochrome c) activity / ethanol catabolic process / outer membrane-bounded periplasmic space / calcium ion binding / membrane
Similarity search - Function
PQQ-dependent type I alcohol dehydrogenase / Bacterial quinoprotein dehydrogenases signature 1. / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / Quinoprotein alcohol dehydrogenase-like superfamily / PQQ-dependent dehydrogenase, methanol/ethanol family / Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain / Pyrrolo-quinoline quinone repeat / Outer membrane protein assembly factor BamB / 8 Propeller ...PQQ-dependent type I alcohol dehydrogenase / Bacterial quinoprotein dehydrogenases signature 1. / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / Quinoprotein alcohol dehydrogenase-like superfamily / PQQ-dependent dehydrogenase, methanol/ethanol family / Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain / Pyrrolo-quinoline quinone repeat / Outer membrane protein assembly factor BamB / 8 Propeller / Methanol Dehydrogenase; Chain A / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / Mainly Beta
Similarity search - Domain/homology
PYRROLOQUINOLINE QUINONE / Quinoprotein ethanol dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsKeitel, T. / Diehl, A. / Knaute, T. / Stezowski, J.J. / Hohne, W. / Gorisch, H.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: X-ray structure of the quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa: basis of substrate specificity.
Authors: Keitel, T. / Diehl, A. / Knaute, T. / Stezowski, J.J. / Hohne, W. / Gorisch, H.
History
DepositionAug 14, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionAug 30, 2000ID: 1EEE
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / 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 / _diffrn_source.pdbx_synchrotron_site / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (QUINOPROTEIN ETHANOL DEHYDROGENASE)
B: PROTEIN (QUINOPROTEIN ETHANOL DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,0678
Polymers128,2472
Non-polymers8216
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-75 kcal/mol
Surface area38710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.400, 159.400, 130.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein PROTEIN (QUINOPROTEIN ETHANOL DEHYDROGENASE)


Mass: 64123.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: Q9Z4J7
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H6N2O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG1500, 50 MM CALCIUM CHLORIDE, 4.5 MM GLYCINE/NAOH PH 8, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
pH: 8 / Details: Stezowski, J.J., (1989) J. Mol. Biol., 205, 617.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
22 mg/mlprotein1drop
34.5 mMglycine-NaOH1drop
41.5 mM1dropCaCl2
50.02 %(w/v)1dropNaCN
622.5 %(v/v)PEG15501reservoir
70.01 %1reservoirNaCN
83 mM1reservoirCaCl2
950 mMglycine-NaOH1reservoir
1ethanol dehydrogenase1drop0.005ml

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 29, 1989
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.52→25.7 Å / Num. obs: 41300 / % possible obs: 94.2 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.33 / % possible all: 98.8
Reflection
*PLUS
Highest resolution: 2.52 Å / Lowest resolution: 25.7 Å / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Num. measured all: 109117 / Rmerge(I) obs: 0.126 / Biso Wilson estimate: 28.2 Å2
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.7 Å / Rmerge(I) obs: 0.36

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
AMoREphasing
REFMACrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 2.6→12.5 Å / σ(F): 1 / σ(I): 1 / Details: MAXIMUM LIKELIHOOD
RfactorNum. reflectionSelection details
Rfree0.274 1476 RANDOM
Rwork0.192 --
obs0.142 28304 -
Refinement stepCycle: LAST / Resolution: 2.6→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9074 0 52 106 9232
Refine LS restraintsType: p_bond_d / Dev ideal: 0.013
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg5

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