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- PDB-2xdr: CRYSTALLOGRAPHIC STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE MUTA... -

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Basic information

Entry
Database: PDB / ID: 2xdr
TitleCRYSTALLOGRAPHIC STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE MUTANT E252A FROM PSEUDOMONAS AERUGINOSA
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: 2.301 Å
AuthorsDiaz-Sanchez, A.G. / Gonzalez-Segura, L. / Rudino-Pinera, E. / Lira-Rocha, A. / Munoz-Clares, R.A.
CitationJournal: To be Published
Title: A Novel Cysteine-Nadph Covalent Adduct in Pseudomonas Aeruginosa Betaine Aldehyde Dehydrogenase Suggests Important Roles for the Reduced Nucleotide in the Reaction Mechanism
Authors: Diaz-Sanchez, A.G. / Gonzalez-Segura, L. / Rudino-Pinera, E. / Lira-Rocha, A. / Munoz-Clares, R.A.
History
DepositionMay 6, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Structure summary / Version format compliance
Revision 1.2Dec 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)217,55231
Polymers212,8044
Non-polymers4,74827
Water30,3011682
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29460 Å2
ΔGint-95 kcal/mol
Surface area56360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.555, 151.555, 242.406
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2437-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
BETAINE ALDEHYDE DEHYDROGENASE / BADH


Mass: 53201.031 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-490 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PCALBETB / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9HTJ1, betaine-aldehyde dehydrogenase

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Non-polymers , 5 types, 1709 molecules

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


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O4
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1682 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 252 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 252 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLU 252 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 252 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 252 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLU 252 TO ALA
Nonpolymer detailsNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP): PART OF THE NADPH MOLECULE IS NOT ...NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP): PART OF THE NADPH MOLECULE IS NOT VISIBLE IN THE ELECTRON DENSITY. FOR THIS REASON SUCH ATOMS ARE NOT PRESENT IN THE MODEL. 2-(2-METHOXYETHOXY)ETHANOL (7P5): 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: 3.77 Å3/Da / Density % sol: 67.4 % / Description: NONE
Crystal growpH: 7.5
Details: CRYSTALS WERE GROWN IN 85 MM HEPES, PH 7.5, 8.5 % (V:V) ISOPROPANOL, 17 % PEG 4000 AND 2 MM 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(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 141370 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 31.77 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.2
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.1 / % possible all: 98.7

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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: 2.301→29.881 Å / SU ML: 0.3 / σ(F): 1.33 / Phase error: 20.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1997 7106 5 %
Rwork0.1603 --
obs0.1623 141370 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.554 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1878 Å20 Å2-0 Å2
2--1.1878 Å2-0 Å2
3----2.3757 Å2
Refinement stepCycle: LAST / Resolution: 2.301→29.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14960 0 211 1682 16853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515670
X-RAY DIFFRACTIONf_angle_d0.94721272
X-RAY DIFFRACTIONf_dihedral_angle_d17.3055833
X-RAY DIFFRACTIONf_chiral_restr0.0662358
X-RAY DIFFRACTIONf_plane_restr0.0042784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.301-2.32710.29562640.22714384X-RAY DIFFRACTION99
2.3271-2.35450.28712220.22644397X-RAY DIFFRACTION98
2.3545-2.38320.26492310.21864415X-RAY DIFFRACTION99
2.3832-2.41330.29182080.21724436X-RAY DIFFRACTION99
2.4133-2.44510.26182360.20734471X-RAY DIFFRACTION99
2.4451-2.47860.2462580.20484365X-RAY DIFFRACTION99
2.4786-2.5140.252350.20434400X-RAY DIFFRACTION99
2.514-2.55150.27722410.20844449X-RAY DIFFRACTION99
2.5515-2.59130.26612350.19544428X-RAY DIFFRACTION99
2.5913-2.63380.22752460.18664395X-RAY DIFFRACTION99
2.6338-2.67910.26512110.18924495X-RAY DIFFRACTION99
2.6791-2.72780.25412290.19334452X-RAY DIFFRACTION99
2.7278-2.78030.24442180.18394418X-RAY DIFFRACTION99
2.7803-2.8370.23652270.17184456X-RAY DIFFRACTION99
2.837-2.89860.20572640.16544437X-RAY DIFFRACTION99
2.8986-2.9660.23282450.17884486X-RAY DIFFRACTION99
2.966-3.04010.21382210.17024451X-RAY DIFFRACTION99
3.0401-3.12220.22052280.17364459X-RAY DIFFRACTION99
3.1222-3.2140.21062490.16254514X-RAY DIFFRACTION99
3.214-3.31760.19292330.15374446X-RAY DIFFRACTION99
3.3176-3.4360.19052550.14344499X-RAY DIFFRACTION99
3.436-3.57330.16992310.13854486X-RAY DIFFRACTION99
3.5733-3.73570.1582360.13054486X-RAY DIFFRACTION99
3.7357-3.93220.14462100.12744563X-RAY DIFFRACTION99
3.9322-4.1780.15622580.12614486X-RAY DIFFRACTION99
4.178-4.49960.14552380.11054504X-RAY DIFFRACTION99
4.4996-4.95050.12752190.10374580X-RAY DIFFRACTION99
4.9505-5.66270.15182740.12744547X-RAY DIFFRACTION100
5.6627-7.11840.18842300.14174656X-RAY DIFFRACTION100
7.1184-29.88380.16012540.14134703X-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)
10.1026-0.0534-0.02260.0864-0.08790.1988-0.00440.00810.01670.08050.02190.0244-0.1337-0.10890.0033-0.0197-0.10020.0095-0.0553-0.03140.043156.8498-51.876165.5476
20.00230.0192-0.00840.09220.03430.12030.05750.002-0.0361-0.0066-0.06590.0718-0.0133-0.14930.01660.02130.04130.01220.228-0.04430.167526.2224-40.634650.6529
30.163-0.0205-0.11880.0641-0.03750.0865-0.00770.3304-0.0851-0.03610.0410.0471-0.0139-0.12370.00470.0576-0.0527-0.05250.3903-0.12220.114248.1171-66.672219.1556
40.1235-0.0228-0.09580.04520.07380.18610.03570.1310.0075-0.05910.01110.0019-0.1307-0.0254-0.03860.1414-0.03220.0170.11970.05740.058866.6666-35.869123.1927
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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