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- PDB-1a4s: BETAINE ALDEHYDE DEHYDROGENASE FROM COD LIVER -

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Basic information

Entry
Database: PDB / ID: 1a4s
TitleBETAINE ALDEHYDE DEHYDROGENASE FROM COD LIVER
ComponentsBETAINE ALDEHYDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ALDEHYDE OXIDATION
Function / homology
Function and homology information


4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / carnitine biosynthetic process / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / cytosol
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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-trimethylaminobutyraldehyde dehydrogenase
Similarity search - Component
Biological speciesGadus callarias (Baltic cod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJohansson, K. / El Ahmad, M. / Hjelmqvist, L. / Ramaswamy, S. / Jornvall, H. / Eklund, H.
CitationJournal: Protein Sci. / Year: 1998
Title: Structure of betaine aldehyde dehydrogenase at 2.1 A resolution.
Authors: Johansson, K. / El-Ahmad, M. / Ramaswamy, S. / Hjelmqvist, L. / Jornvall, H. / Eklund, H.
History
DepositionFeb 3, 1998Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
C: BETAINE ALDEHYDE DEHYDROGENASE
D: BETAINE ALDEHYDE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)217,6904
Polymers217,6904
Non-polymers00
Water12,484693
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21140 Å2
ΔGint-111 kcal/mol
Surface area62060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.170, 86.220, 88.330
Angle α, β, γ (deg.)105.20, 115.13, 100.02
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.893645, -0.448756, -0.004025), (-0.448629, -0.893548, 0.017429), (-0.011418, -0.01377, -0.99984)0.10967, -0.15199, -0.54411
2given(-0.921968, 0.332427, -0.198666), (0.335847, 0.4309, -0.837575), (-0.192827, -0.838938, -0.508921)-0.19659, 0.08797, -0.21101
3given(-0.972278, 0.101455, 0.210672), (0.123349, -0.542874, 0.830706), (0.198648, 0.833663, 0.51531)0.03417, 0.43536, 0.17824

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Components

#1: Protein
BETAINE ALDEHYDE DEHYDROGENASE / ALDH


Mass: 54422.398 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Gadus callarias (Baltic cod) / Organ: LIVER / References: UniProt: P56533, betaine-aldehyde dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / 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: 2.43 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 287 K / pH: 7.5
Details: PROTEIN WAS CRYSTALLIZED AT 14 DEGREES FROM 20% PEG 4000, 9.5% ISOPROPANOL, 100 MM HEPES, PH 7.5, temperature 287K
Crystal grow
*PLUS
Temperature: 14 ℃ / pH: 7.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 MHEPES1reservoir
29.5 %isopropanol1reservoir
320 %PEG40001reservoir
44 mg/mlprotein1drop
51 mMNAD+1drop
620 mMBis-Tris1drop
7150 mM1dropNaCl
80.1 mMDTE1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.7684
DetectorType: PRINCETON 2K / Detector: CCD / Date: Mar 2, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7684 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 90475 / % possible obs: 75.8 % / Observed criterion σ(I): 5 / Redundancy: 1.6 % / Biso Wilson estimate: 14.6 Å2 / Rsym value: 0.056 / Net I/σ(I): 15.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.05 % / Mean I/σ(I) obs: 5 / Rsym value: 0.104 / % possible all: 38.6
Reflection
*PLUS
Rmerge(I) obs: 0.056

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AG8

1ag8


Resolution: 2.1→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2224532 / Data cutoff high rms absF: 2224532 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1789 2 %RANDOM
Rwork0.223 ---
obs0.223 88476 75.2 %-
Displacement parametersBiso mean: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.92 Å20.13 Å2-0.49 Å2
2--3.08 Å21.1 Å2
3----0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15777 0 0 693 16470
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 153 1.9 %
Rwork0.23 7734 -
obs--40.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.74
LS refinement shell
*PLUS
Rfactor Rwork: 0.23

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