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- PDB-6b4r: The crystal structure of the aldehyde dehydrogenase KauB from Pse... -

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Basic information

Entry
Database: PDB / ID: 6b4r
TitleThe crystal structure of the aldehyde dehydrogenase KauB from Pseudomonas aeruginosa
Components(KauB) x 2
KeywordsOXIDOREDUCTASE / aldehyde dehydrogenase / KauB
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Probable aldehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsGonzalez-Segura, L. / Cardona-Cardona, Y. / Carrillo-Campos, J. / Munoz-Clares, R.A.
Funding support Mexico, 1items
OrganizationGrant numberCountry
PAPIITIN-220317 Mexico
CitationJournal: To Be Published
Title: Aldehyde specificity of the aldehyde dehydrogenase KauB from Pseudomonas aeruginosa: Critical amino acid residues revealed by its crystal structure
Authors: Cardona-Cardona, Y. / Gonzalez-Segura, L. / Carrillo-Campos, J. / Regla, I. / Lopez-Ortiz, M. / Gutierrez, A. / Munoz-Clares, R.A.
History
DepositionSep 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KauB
B: KauB
C: KauB
D: KauB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,85916
Polymers212,8704
Non-polymers98912
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21240 Å2
ΔGint-96 kcal/mol
Surface area60780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.637, 93.811, 128.864
Angle α, β, γ (deg.)90.00, 92.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein KauB / Probable aldehyde dehydrogenase


Mass: 53233.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA5312 / Plasmid: pET28b-KauB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): Rosetta DE3
References: UniProt: Q9HTP2, gamma-guanidinobutyraldehyde dehydrogenase
#2: Protein KauB / Probable aldehyde dehydrogenase


Mass: 53201.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA5312 / Plasmid: pET28b-KauB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): Rosetta DE3
References: UniProt: Q9HTP2, gamma-guanidinobutyraldehyde dehydrogenase

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Non-polymers , 5 types, 528 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H16O4
#6: 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.17 M SODIUM ACETATE TRIHYDRATE, 0.1 M TRIS HYDROCHLORIDE PH 8.5, 25.5% W/V POLYETHYLENE GLYCOL 4,000, 15% V/V GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.55→46.125 Å / Num. obs: 68734 / % possible obs: 99.41 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.049 / Net I/σ(I): 10.5
Reflection shellResolution: 2.55→2.641 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 10041 / Rpim(I) all: 0.158 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LIH

4lih


Resolution: 2.55→46.125 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2335 3484 5.07 %
Rwork0.1778 --
obs0.1806 68734 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→46.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14923 0 58 516 15497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215306
X-RAY DIFFRACTIONf_angle_d0.59420773
X-RAY DIFFRACTIONf_dihedral_angle_d11.1765523
X-RAY DIFFRACTIONf_chiral_restr0.0412371
X-RAY DIFFRACTIONf_plane_restr0.0032686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.58490.32631420.24952601X-RAY DIFFRACTION100
2.5849-2.62190.24791220.2322599X-RAY DIFFRACTION100
2.6219-2.6610.33731320.2172615X-RAY DIFFRACTION100
2.661-2.70260.29091420.21062603X-RAY DIFFRACTION99
2.7026-2.74690.24371370.20872600X-RAY DIFFRACTION100
2.7469-2.79420.27981500.20932591X-RAY DIFFRACTION100
2.7942-2.8450.29291300.19972606X-RAY DIFFRACTION99
2.845-2.89970.26231530.20072578X-RAY DIFFRACTION100
2.8997-2.95890.23851260.20672631X-RAY DIFFRACTION100
2.9589-3.02320.26071590.22595X-RAY DIFFRACTION99
3.0232-3.09360.25471540.20072535X-RAY DIFFRACTION99
3.0936-3.17090.27481450.20972597X-RAY DIFFRACTION99
3.1709-3.25660.30681220.20982615X-RAY DIFFRACTION98
3.2566-3.35240.25341420.20692595X-RAY DIFFRACTION100
3.3524-3.46060.27651560.19562618X-RAY DIFFRACTION100
3.4606-3.58420.26281400.1882576X-RAY DIFFRACTION100
3.5842-3.72770.23651600.17732604X-RAY DIFFRACTION100
3.7277-3.89720.261400.16462607X-RAY DIFFRACTION100
3.8972-4.10260.18891500.15372600X-RAY DIFFRACTION100
4.1026-4.35950.21621090.15182660X-RAY DIFFRACTION100
4.3595-4.69580.15981380.13812583X-RAY DIFFRACTION98
4.6958-5.16770.20091290.14732635X-RAY DIFFRACTION99
5.1677-5.91420.20311290.1582672X-RAY DIFFRACTION100
5.9142-7.44620.20391420.16552626X-RAY DIFFRACTION100
7.4462-46.13220.15141350.14042708X-RAY DIFFRACTION99

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