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- PDB-4cvb: Crystal structure of quinone-dependent alcohol dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 4cvb
TitleCrystal structure of quinone-dependent alcohol dehydrogenase from Pseudogluconobacter saccharoketogenenes
ComponentsALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / CARBOHYDRATE OXIDATION / QUINOPROTEIN
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
Similarity search - Function
Quinoprotein alcohol dehydrogenase-like superfamily / Pyrrolo-quinoline quinone repeat / PQQ-like domain / 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
PROPANOIC ACID / PYRROLOQUINOLINE QUINONE / Alcohol dehydrogenase
Similarity search - Component
Biological speciesPSEUDOGLUCONOBACTER SACCHAROKETOGENES (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsRozeboom, H.J. / Yu, S. / Mikkelsen, R. / Nikolaev, I. / Mulder, H. / Dijkstra, B.W.
CitationJournal: Protein Sci. / Year: 2015
Title: Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase from Pseudogluconobacter Saccharoketogenes. A Versatile Dehydrogenase Oxidizing Alcohols and Carbohydrates.
Authors: Rozeboom, H.J. / Yu, S. / Mikkelsen, R. / Nikolaev, I. / Mulder, H.J. / Dijkstra, B.W.
History
DepositionMar 25, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1059
Polymers61,3641
Non-polymers7418
Water11,277626
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: ALCOHOL DEHYDROGENASE
hetero molecules

A: ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,21118
Polymers122,7282
Non-polymers1,48316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4730 Å2
ΔGint-249.7 kcal/mol
Surface area34360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.950, 87.190, 57.100
Angle α, β, γ (deg.)90.00, 90.16, 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 ALCOHOL DEHYDROGENASE / QUINONE-DEPENDENT ALCOHOL DEHYDROGENASE


Mass: 61363.812 Da / Num. of mol.: 1 / Fragment: RESIDUES 37-608
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOGLUCONOBACTER SACCHAROKETOGENES (bacteria)
Strain: IFO 14464 / Plasmid: PPIC2-ADH / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): GS115
References: UniProt: Q93RE9, alcohol dehydrogenase (cytochrome c)

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Non-polymers , 6 types, 634 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


Mass: 330.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H6N2O8
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsN-TERMINUS OF MATURE PROTEIN STARTS AT POSITION 37 (AEPSK.. )

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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: 51 % / Description: NONE
Crystal growpH: 7
Details: 18-21% PEG550 MME, 20 MM ZN(AC)2, 100 MM PCB BUFFER PH 6-7

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 2, 2009 / Details: OXMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.773
11h,-k,-l20.227
ReflectionResolution: 1.72→30.5 Å / Num. obs: 59031 / % possible obs: 88.9 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.4
Reflection shellResolution: 1.72→1.84 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.3 / % possible all: 31.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1KB0 AND 1YIQ

1kb0

1yiq


Resolution: 1.72→27.95 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.035 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.14858 2924 5 %RANDOM
Rwork0.1277 ---
obs0.12872 56104 88.95 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.709 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å21.55 Å2
2---4.16 Å20 Å2
3---5.87 Å2
Refinement stepCycle: LAST / Resolution: 1.72→27.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4251 0 35 626 4912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024432
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.956042
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9685569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5624.607191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70315649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7381522
X-RAY DIFFRACTIONr_chiral_restr0.0870.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213466
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.721→1.766 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 12 -
Rwork0.231 291 -
obs--6.3 %
Refinement TLS params.Method: refined / Origin x: 23.19 Å / Origin y: 29.784 Å / Origin z: 21.15 Å
111213212223313233
T0.0357 Å20.0018 Å2-0.0155 Å2-0.0201 Å2-0.0025 Å2--0.0088 Å2
L0.5076 °20.1915 °2-0.1629 °2-0.3429 °2-0.1 °2--0.4706 °2
S-0.0177 Å °0.0127 Å °-0.0042 Å °-0.0234 Å °0.016 Å °-0.0029 Å °-0.0259 Å °0.0137 Å °0.0018 Å °

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