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- PDB-1kb0: Crystal Structure of Quinohemoprotein Alcohol Dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 1kb0
TitleCrystal Structure of Quinohemoprotein Alcohol Dehydrogenase from Comamonas testosteroni
Componentsquinohemoprotein alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / beta-propeller fold / cytochrome c
Function / homology
Function and homology information


alcohol dehydrogenase (azurin) / oxidoreductase activity, acting on CH-OH group of donors / outer membrane-bounded periplasmic space / electron transfer activity / calcium ion binding / heme binding / membrane
Similarity search - Function
Quinoprotein alcohol dehydrogenase-like superfamily / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / 8 Propeller / Methanol Dehydrogenase; Chain A ...Quinoprotein alcohol dehydrogenase-like superfamily / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / 8 Propeller / Methanol Dehydrogenase; Chain A / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Quinoprotein alcohol dehydrogenase-like superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
HEME C / PYRROLOQUINOLINE QUINONE / TETRAHYDROFURAN-2-CARBOXYLIC ACID / Quinohemoprotein alcohol dehydrogenase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsRozeboom, H.J. / Oubrie, A.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of quinohemoprotein alcohol dehydrogenase from Comamonas testosteroni: structural basis for substrate oxidation and electron transfer.
Authors: Oubrie, A. / Rozeboom, H.J. / Kalk, K.H. / Huizinga, E.G. / Dijkstra, B.W.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2001
Title: Crystallization of quinohaemoprotein alcohol dehydrogenase from Comamonas testosteroni: crystals with unique optical properties.
Authors: Oubrie, A. / Huizinga, E.G. / Rozeboom, H.J. / Kalk, K.H. / de Jong, G.A. / Duine, J.A. / Dijkstra, B.W.
History
DepositionNov 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _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: quinohemoprotein alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8208
Polymers73,4381
Non-polymers1,3817
Water18,3031016
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.920, 74.331, 92.332
Angle α, β, γ (deg.)90.00, 105.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein quinohemoprotein alcohol dehydrogenase / quinohemoprotein ethanol dehydrogenase type 1


Mass: 73438.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Comamonas testosteroni (bacteria) / References: UniProt: Q46444, EC: 1.1.99.-

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Non-polymers , 6 types, 1023 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-TFB / TETRAHYDROFURAN-2-CARBOXYLIC ACID / Tetrahydro-2-furoic acid


Mass: 116.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O3
#5: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE / Pyrroloquinoline quinone


Mass: 330.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H6N2O8
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1016 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: PEG 6000, MES, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Details: Oubrie, A., (2001) ACTA CRYSTALLOGR.,SECT.D, 57, 1732.
PH range low: 5.7 / PH range high: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-8 mg/mlprotein1drop
217-20 %(w/v)PEG60001reservoir
30-4 mMEDTA1reservoir
4100 mMMES1reservoirpH5.5-5.7

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11201
21
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9076 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 27, 1998
RadiationProtocol: OSCILLATION / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9076 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. obs: 111086 / % possible obs: 96.2 % / Redundancy: 2.2 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 16
Reflection shellResolution: 1.44→1.46 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2 / Rsym value: 0.34 / % possible all: 87.7
Reflection shell
*PLUS
% possible obs: 87.7 % / Rmerge(I) obs: 0.34

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EEE (now known as 1FLG)

1eee
PDB Unreleased entry

1flg


Resolution: 1.44→29.63 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1721072.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: HOH 492 belongs to conformation A of ASP 657.
RfactorNum. reflection% reflectionSelection details
Rfree0.188 5671 5.1 %RANDOM
Rwork0.16 ---
obs0.16 111086 96.3 %-
all-111086 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.9357 Å2 / ksol: 0.377884 e/Å3
Displacement parametersBiso mean: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.25 Å20 Å23.33 Å2
2---1.93 Å20 Å2
3----2.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.44→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5128 0 94 1016 6238
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
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_deg2.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.37
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.642
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.452.5
LS refinement shellResolution: 1.44→1.53 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 930 5.1 %
Rwork0.228 17480 -
obs--96.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PQQ.PARWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMTOPH19.HEM
X-RAY DIFFRACTION4ION.PARAMPQQ.TOP
X-RAY DIFFRACTION5PARAM19X.HEMEION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.16 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.37
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_mcangle_it1.642
X-RAY DIFFRACTIONc_scangle_it2.452.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.259 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.228

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