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- PDB-3k2w: CRYSTAL STRUCTURE OF betaine-aldehyde dehydrogenase FROM Pseudoal... -

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Basic information

Entry
Database: PDB / ID: 3k2w
TitleCRYSTAL STRUCTURE OF betaine-aldehyde dehydrogenase FROM Pseudoalteromonas atlantica T6c
ComponentsBetaine-aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PSI-2 / ALDEHYDE DEHYDROGENASE / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC
Function / homology
Function and homology information


betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity
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
ACETATE ION / Betaine-aldehyde dehydrogenase
Similarity search - Component
Biological speciesPseudoalteromonas atlantica T6c (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsPatskovsky, Y. / Toro, R. / Rutter, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF betaine-aldehyde dehydrogenase FROM Pseudoalteromonas atlantica
Authors: Patskovsky, Y. / Toro, R. / Rutter, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionSep 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
E: Betaine-aldehyde dehydrogenase
F: Betaine-aldehyde dehydrogenase
G: Betaine-aldehyde dehydrogenase
H: Betaine-aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)434,71739
Polymers432,5148
Non-polymers2,20331
Water29,0401612
1
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)217,37220
Polymers216,2574
Non-polymers1,11516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21130 Å2
ΔGint-133 kcal/mol
Surface area59880 Å2
MethodPISA
2
E: Betaine-aldehyde dehydrogenase
F: Betaine-aldehyde dehydrogenase
G: Betaine-aldehyde dehydrogenase
H: Betaine-aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,34619
Polymers216,2574
Non-polymers1,08915
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21290 Å2
ΔGint-135 kcal/mol
Surface area60150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.785, 163.718, 142.069
Angle α, β, γ (deg.)90.00, 90.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

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Components

#1: Protein
Betaine-aldehyde dehydrogenase /


Mass: 54064.234 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas atlantica T6c (bacteria)
Strain: T6c / BAA-1087 / Gene: Patl_2553 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15SR9, betaine-aldehyde dehydrogenase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1612 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 294 K / pH: 4.6
Details: 0.1M SODIUM ACETATE, PH 4.6, 30% PEG4000, 200MM AMMONIUM ACETATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 24, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 310867 / % possible obs: 98.8 % / Observed criterion σ(I): -5 / Redundancy: 2.6 % / Biso Wilson estimate: 30.32 Å2 / Rsym value: 0.113 / Net I/σ(I): 3.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 0.5 / % possible all: 97

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.3.0034refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.59 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 9231 3 %RANDOM
Rwork0.21 ---
obs0.212 293687 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-0.65 Å2
2---1.79 Å20 Å2
3---1.4 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29404 0 134 1612 31150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02230360
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.96141186
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20753956
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53725.9361309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.494155258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6251593
X-RAY DIFFRACTIONr_chiral_restr0.0970.24680
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222804
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1610.315695
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.520668
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.53728
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.373
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.522
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.89219852
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.091331118
X-RAY DIFFRACTIONr_scbond_it10.018411839
X-RAY DIFFRACTIONr_scangle_it11.858610020
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3436 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.40.3
medium positional0.390
medium positional0.30
medium positional0.340
medium positional0.310
medium positional0.280
medium positional0.30
medium positional0.340
medium thermal13.327.5
medium thermal70
medium thermal8.30
medium thermal6.750
medium thermal7.720
medium thermal8.50
medium thermal6.540
medium thermal9.80
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 552 -
Rwork0.324 17145 -
obs--77.73 %

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