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- PDB-5min: Apo form of the soluble PQQ-dependent Glucose Dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 5min
TitleApo form of the soluble PQQ-dependent Glucose Dehydrogenase from Acinetobacter calcoaceticus
ComponentsQuinoprotein glucose dehydrogenase B
KeywordsOXIDOREDUCTASE / Dehydrogenase / Apo form
Function / homology
Function and homology information


glucose 1-dehydrogenase (PQQ, quinone) / quinoprotein glucose dehydrogenase activity / metal ion binding
Similarity search - Function
PQQ-dependent dehydrogenase, s-GDH family / Glucose/Sorbosone dehydrogenase / Glucose / Sorbosone dehydrogenase / Soluble quinoprotein glucose/sorbosone dehydrogenase / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Quinoprotein glucose dehydrogenase B
Similarity search - Component
Biological speciesAcinetobacter calcoaceticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 Å
AuthorsStines-Chaumeil, C. / Mavre, F. / Limoges, B. / Kauffmann, B. / Mano, N.
CitationJournal: To Be Published
Title: Apo form of the soluble PQQ-dependent Glucose Dehydrogenase from Acinetobacter calcoaceticus
Authors: Stines-Chaumeil, C. / Mavre, F. / Limoges, B. / Kauffmann, B. / Mano, N.
History
DepositionNov 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 17, 2024Group: 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
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_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Quinoprotein glucose dehydrogenase B
B: Quinoprotein glucose dehydrogenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4889
Polymers100,2122
Non-polymers2767
Water19,7981099
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-83 kcal/mol
Surface area34490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.407, 54.898, 85.474
Angle α, β, γ (deg.)88.040, 81.580, 69.620
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Quinoprotein glucose dehydrogenase B / Glucose dehydrogenase B [pyrroloquinoline-quinone] / Soluble glucose dehydrogenase / s-GDH


Mass: 50105.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter calcoaceticus (bacteria) / Gene: gdhB / Plasmid: pp2418 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P13650, glucose 1-dehydrogenase (PQQ, quinone)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1099 / 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: 2.36 Å3/Da / Density % sol: 47.92 % / Description: Prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 4000 (12%) 100 mM TRIS pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 3, 2014 / Details: OSMIC VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.76→25.73 Å / Num. obs: 83379 / % possible obs: 91.6 % / Redundancy: 3.07 % / Net I/σ(I): 9.42

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
XSCALEdata reduction
PHASERphasing
BUSTERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C9U

1c9u


Resolution: 1.76→25.73 Å / Cor.coef. Fo:Fc: 0.9584 / Cor.coef. Fo:Fc free: 0.9414 / SU R Cruickshank DPI: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.138 / SU Rfree Blow DPI: 0.126 / SU Rfree Cruickshank DPI: 0.122
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 4137 4.96 %RANDOM
Rwork0.1776 ---
obs0.1795 83379 91.74 %-
Displacement parametersBiso max: 102.43 Å2 / Biso mean: 20.23 Å2 / Biso min: 5.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.6439 Å2-1.2862 Å20.4221 Å2
2---1.8344 Å20.217 Å2
3---1.1905 Å2
Refine analyzeLuzzati coordinate error obs: 0.207 Å
Refinement stepCycle: final / Resolution: 1.76→25.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7073 0 7 1099 8179
Biso mean--21.16 30.56 -
Num. residues----905
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2478SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes199HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1056HARMONIC5
X-RAY DIFFRACTIONt_it7329HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion955SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9205SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7329HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10002HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion4.02
X-RAY DIFFRACTIONt_other_torsion16.14
LS refinement shellResolution: 1.76→1.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3232 246 5.11 %
Rwork0.2794 4572 -
all0.2816 4818 -
obs--72.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3235-0.13490.03390.28930.14380.66360.01160.08360.0117-0.0219-0.03070.00020.0072-0.02230.0191-0.038-0.0112-0.0042-0.0368-0.0061-0.029520.026419.329375.803
20.3214-0.05660.01440.4712-0.04870.5498-0.0286-0.0691-0.01090.05890.0081-0.01-0.0023-0.02530.0205-0.04450.0061-0.0202-0.0297-0.0172-0.038528.76162.8951112.0442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 452
2X-RAY DIFFRACTION2{ B|* }B1 - 453

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