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- PDB-1kv9: Structure at 1.9 A Resolution of a Quinohemoprotein Alcohol Dehyd... -

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Basic information

Entry
Database: PDB / ID: 1kv9
TitleStructure at 1.9 A Resolution of a Quinohemoprotein Alcohol Dehydrogenase from Pseudomonas putida HK5
ComponentsTYPE II QUINOHEMOPROTEIN ALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / Quinohemoprotein Alcohol Dehydrogenase / electron transfer
Function / homology
Function and homology information


alcohol dehydrogenase (azurin) / pyrroloquinoline quinone binding / oxidoreductase activity, acting on CH-OH group of donors / outer membrane-bounded periplasmic space / electron transfer activity / oxidoreductase activity / calcium ion binding / heme binding / membrane / metal ion binding
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 / Quinoprotein alcohol dehydrogenase-like superfamily / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETONE / HEME C / PYRROLOQUINOLINE QUINONE / Quinohemoprotein alcohol dehydrogenase ADH IIB
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / molecular replacement, MIR, MAD / Resolution: 1.9 Å
AuthorsChen, Z.-W. / Matsushita, K. / Yamashita, T. / Fujii, T. / Toyama, H. / Adachi, O. / Bellamy, H.D. / Mathews, F.S.
Citation
Journal: Structure / Year: 2002
Title: Structure at 1.9 A resolution of a quinohemoprotein alcohol dehydrogenase from Pseudomonas putida HK5.
Authors: Chen, Z.W. / Matsushita, K. / Yamashita, T. / Fujii, T.A. / Toyama, H. / Adachi, O. / Bellamy, H.D. / Mathews, F.S.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Determination of the Gene Sequence and the Three-dimensional Structure at 2.4 Angstroms Resolution of Methanol Dehydrogenase from Methylophilus W3A1
Authors: Xia, Z. / Dai, W. / Zhang, Y. / White, S.A. / Boyd, G.D. / Mathews, F.S.
History
DepositionJan 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999sequence an appropriate sequence database reference was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYPE II QUINOHEMOPROTEIN ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0867
Polymers72,7091
Non-polymers1,3776
Water13,187732
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.807, 57.437, 67.523
Angle α, β, γ (deg.)89.65, 69.34, 68.39
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TYPE II QUINOHEMOPROTEIN ALCOHOL DEHYDROGENASE


Mass: 72709.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / References: UniProt: Q8GR64, EC: 1.1.99.-

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Non-polymers , 7 types, 738 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE / Pyrroloquinoline quinone


Mass: 330.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H6N2O8
#4: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-ACN / ACETONE / Acetone


Mass: 58.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 732 / 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: 2.74 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 8000, sodium citrate, HEPES, 2-propanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K
Crystal grow
*PLUS
Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17.5 mg/mlprotein1drop
214-22 %PEG80001reservoir
3150 mMsodium citrate1reservoir
4100 mMHEPES-NaOH1reservoirpH7.5
56 %2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 15, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 48675 / Num. obs: 48672 / % possible obs: 87.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2643 / % possible all: 47.3
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 47.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoRE+ SHARPphasing
CNSrefinement
SHARPphasing
RefinementMethod to determine structure: molecular replacement, MIR, MAD
Starting model: PDB ENTRY 4AAH

4aah


Resolution: 1.9→30 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.189 4922 10 %RANDOM
Rwork0.154 ---
all-55885 --
obs-48672 87.1 %-
Displacement parametersBiso mean: 21.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5103 0 93 732 5928
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.9-2.020.2484940.23X-RAY DIFFRACTION45426
2.02-2.170.2358200.189X-RAY DIFFRACTION74376
2.17-2.390.2118690.16X-RAY DIFFRACTION76906
2.39-2.740.1948930.157X-RAY DIFFRACTION78446
2.74-3.450.1919360.149X-RAY DIFFRACTION79966
3.45-300.1579100.133X-RAY DIFFRACTION82416
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Rfactor Rwork: 0.23

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