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- PDB-3zqa: CRYSTALLOGRAPHIC STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE MUTA... -

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Basic information

Entry
Database: PDB / ID: 3zqa
TitleCRYSTALLOGRAPHIC STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE MUTANT C286A FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH NADPH
ComponentsBETAINE ALDEHYDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ALDEHYDE OXIDATION / NADPH COMPLEX
Function / homology
Function and homology information


betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / metal ion binding
Similarity search - Function
Betaine aldehyde dehydrogenase / 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 ...Betaine aldehyde dehydrogenase / 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
: / Chem-NDP / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / NAD/NADP-dependent betaine aldehyde dehydrogenase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsDiaz-Sanchez, A.G. / Gonzalez-Segura, L. / Rudino-Pinera, E. / Lira-Rocha, A. / Torres-Larios, A. / Munoz-Clares, R.A.
CitationJournal: Biochem.J. / Year: 2011
Title: Novel Nadph-Cysteine Covalent Adduct Found in the Active Site of an Aldehyde Dehydrogenase.
Authors: Diaz-Sanchez, A.G. / Gonzalez-Segura, L. / Rudino-Pinera, E. / Lira-Rocha, A. / Torres-Larios, A. / Munoz-Clares, R.A.
History
DepositionJun 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 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_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.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.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.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_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: BETAINE ALDEHYDE DEHYDROGENASE
B: BETAINE ALDEHYDE DEHYDROGENASE
C: BETAINE ALDEHYDE DEHYDROGENASE
D: BETAINE ALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,32843
Polymers213,4334
Non-polymers5,89539
Water34,0661891
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35360 Å2
ΔGint-100.8 kcal/mol
Surface area54840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.439, 151.439, 241.752
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
BETAINE ALDEHYDE DEHYDROGENASE / BADH


Mass: 53358.199 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PCALBETB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9HTJ1, betaine-aldehyde dehydrogenase

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Non-polymers , 7 types, 1930 molecules

#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1891 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 286 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 286 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, CYS 286 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 286 TO ALA ENGINEERED RESIDUE IN CHAIN C, CYS 286 TO ALA ENGINEERED RESIDUE IN CHAIN D, CYS 286 TO ALA
Nonpolymer details1,2-ETHANEDIOL (EDO): FRAGMENT OF A PEG MOLECULE VISIBLE IN THE ELECTRON DENSITY. TETRAETHYLENE ...1,2-ETHANEDIOL (EDO): FRAGMENT OF A PEG MOLECULE VISIBLE IN THE ELECTRON DENSITY. TETRAETHYLENE GLYCOL (PG4): FRAGMENT OF A PEG MOLECULE VISIBLE IN THE ELECTRON DENSITY. 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL (TOE): FRAGMENT OF A PEG MOLECULE VISIBLE IN THE ELECTRON DENSITY.

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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: 3.81 Å3/Da / Density % sol: 67.7 % / Description: NONE
Crystal growpH: 7.5
Details: CRYSTALS WERE GROWN IN 85 MM HEPES PH 7.5, 8.5% (V:V) ISOPROPANOL, 17% (W:V)PEG 4000, 15% (V:V) GLYCEROL AND 2MM NADPH.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 20, 2010 / Details: DOUBLE CRYSTAL CHANNEL CUT, SI(III) 1M LONG
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 117977 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 38.67 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7
Reflection shellResolution: 2.45→2.5 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WME

2wme


Resolution: 2.45→38.515 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 18.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1906 5938 5 %
Rwork0.1551 --
obs0.1569 117977 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.906 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8951 Å20 Å20 Å2
2--2.8951 Å20 Å2
3----5.7901 Å2
Refinement stepCycle: LAST / Resolution: 2.45→38.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14972 0 370 1891 17233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01115923
X-RAY DIFFRACTIONf_angle_d1.40921629
X-RAY DIFFRACTIONf_dihedral_angle_d20.3755864
X-RAY DIFFRACTIONf_chiral_restr0.1682432
X-RAY DIFFRACTIONf_plane_restr0.0052766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.47780.2741880.2253719X-RAY DIFFRACTION100
2.4778-2.5070.26712040.22013632X-RAY DIFFRACTION100
2.507-2.53760.27952100.21063691X-RAY DIFFRACTION100
2.5376-2.56970.2882010.21553743X-RAY DIFFRACTION100
2.5697-2.60350.24642230.19733656X-RAY DIFFRACTION100
2.6035-2.63910.22871890.19013703X-RAY DIFFRACTION100
2.6391-2.67680.23282050.17783672X-RAY DIFFRACTION100
2.6768-2.71680.24521760.17833751X-RAY DIFFRACTION100
2.7168-2.75920.23391910.18353678X-RAY DIFFRACTION100
2.7592-2.80440.24091940.17923748X-RAY DIFFRACTION100
2.8044-2.85280.24371810.17493725X-RAY DIFFRACTION100
2.8528-2.90460.2322110.16823677X-RAY DIFFRACTION100
2.9046-2.96050.21911930.16893708X-RAY DIFFRACTION100
2.9605-3.02090.21462120.16453694X-RAY DIFFRACTION100
3.0209-3.08660.23351880.16243738X-RAY DIFFRACTION100
3.0866-3.15830.1962070.1613733X-RAY DIFFRACTION100
3.1583-3.23730.20612060.15093698X-RAY DIFFRACTION100
3.2373-3.32470.19141840.14653701X-RAY DIFFRACTION100
3.3247-3.42250.19121910.14123735X-RAY DIFFRACTION100
3.4225-3.53290.1881680.13583783X-RAY DIFFRACTION100
3.5329-3.65910.15051820.13083735X-RAY DIFFRACTION100
3.6591-3.80550.1651910.12693757X-RAY DIFFRACTION100
3.8055-3.97850.15832130.11953733X-RAY DIFFRACTION100
3.9785-4.1880.14222040.11473742X-RAY DIFFRACTION100
4.188-4.45010.1322220.10383765X-RAY DIFFRACTION100
4.4501-4.79310.13341910.09883730X-RAY DIFFRACTION100
4.7931-5.27430.13291900.1123824X-RAY DIFFRACTION100
5.2743-6.0350.18561900.14183818X-RAY DIFFRACTION100
6.035-7.59390.15852170.15153835X-RAY DIFFRACTION100
7.5939-38.52010.16132160.1573915X-RAY DIFFRACTION98
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)
10.1658-0.07920.06780.3199-0.04210.28070.0480.05590.0047-0.0467-0.04450.00120.03350.0206-0.00520.10120.015-0.00350.1663-0.02350.131959.131-56.0022-25.5337
20.35750.1166-0.01390.15070.12010.28170.00130.0029-0.12010.04560.0156-0.02520.1487-0.0155-0.0210.1798-0.028-0.01160.0642-0.00650.162753.4431-88.4034-10.8344
30.284-0.02570.07570.43090.00720.43960.0935-0.1704-0.01670.1998-0.06420.06920.0629-0.0854-0.02330.2593-0.12570.04910.30610.00120.188542.2702-56.242421.2306
40.22250.07870.03620.29330.06680.38050.0721-0.0616-0.00530.0898-0.0454-0.05220.04940.1082-0.02110.1504-0.0187-0.04320.25230.02010.141378.2023-55.665117.1434
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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