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- PDB-3r31: Crystal structure of betaine aldehyde dehydrogenase from Agrobact... -

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Basic information

Entry
Database: PDB / ID: 3r31
TitleCrystal structure of betaine aldehyde dehydrogenase from Agrobacterium tumefaciens
ComponentsBetaine aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / betaine aldehyde dehydrogenase
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
NAD/NADP-dependent betaine aldehyde dehydrogenase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.148 Å
AuthorsAgarwal, R. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of betaine aldehyde dehydrogenase from Agrobacterium tumefaciens
Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S.
History
DepositionMar 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Betaine aldehyde dehydrogenase
B: Betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,7474
Polymers110,6232
Non-polymers1242
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-19 kcal/mol
Surface area34050 Å2
MethodPISA
2
A: Betaine aldehyde dehydrogenase
B: Betaine aldehyde dehydrogenase
hetero molecules

A: Betaine aldehyde dehydrogenase
B: Betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,4958
Polymers221,2464
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area16360 Å2
ΔGint-54 kcal/mol
Surface area60450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.879, 98.879, 174.578
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Betaine aldehyde dehydrogenase / BADH


Mass: 55311.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / ATCC 33970 / Gene: betB, Atu0829, AGR_C_1515 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q8UH56, betaine-aldehyde dehydrogenase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M MgCl2, 0.1M Bis-tris pH 6.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9891 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2010 / Details: mirrors
RadiationMonochromator: Si-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9891 Å / Relative weight: 1
ReflectionResolution: 2.148→50 Å / Num. all: 54545 / Num. obs: 54545 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 21.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.8
Reflection shellResolution: 2.148→2.23 Å / Redundancy: 21 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4 / Num. unique all: 3740 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.148→43.02 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.242 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.244 / ESU R Free: 0.202 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24526 2767 5.1 %RANDOM
Rwork0.19422 ---
obs0.1968 51767 99.92 %-
all-54545 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.232 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.148→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7133 0 8 219 7360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0227286
X-RAY DIFFRACTIONr_angle_refined_deg1.9431.9659892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8635962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.93324.605291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.734151148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.691536
X-RAY DIFFRACTIONr_chiral_restr0.1460.21120
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215541
X-RAY DIFFRACTIONr_mcbond_it1.0731.54770
X-RAY DIFFRACTIONr_mcangle_it1.92327605
X-RAY DIFFRACTIONr_scbond_it3.46532516
X-RAY DIFFRACTIONr_scangle_it5.2824.52287
LS refinement shellResolution: 2.148→2.204 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 196 -
Rwork0.215 3769 -
obs-3740 99.47 %

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