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

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Basic information

Entry
Database: PDB / ID: 1bpw
TitleBETAINE ALDEHYDE DEHYDROGENASE FROM COD LIVER
ComponentsPROTEIN (ALDEHYDE DEHYDROGENASE)
KeywordsOXIDOREDUCTASE / ALDEHYDE OXIDATION / NAD COMPLEX
Function / homology
Function and homology information


4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / carnitine biosynthetic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / 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, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 4-trimethylaminobutyraldehyde dehydrogenase
Similarity search - Component
Biological speciesGadus callarias (Baltic cod)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJohansson, K. / El Ahmad, M. / Ramaswamy, S. / Hjelmqvist, L. / 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
DepositionAug 12, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 19, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (ALDEHYDE DEHYDROGENASE)
B: PROTEIN (ALDEHYDE DEHYDROGENASE)
C: PROTEIN (ALDEHYDE DEHYDROGENASE)
D: PROTEIN (ALDEHYDE DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,3438
Polymers217,6904
Non-polymers2,6544
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25880 Å2
ΔGint-149 kcal/mol
Surface area59930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.400, 86.570, 89.810
Angle α, β, γ (deg.)105.32, 113.29, 98.16
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.8594, -0.50651, -0.06986), (-0.50641, -0.86205, 0.02044), (-0.07058, 0.01781, -0.99735)0.0093, -0.0851, 0.0817
2given(-0.91262, 0.35147, -0.20879), (0.35305, 0.42011, -0.83598), (-0.20611, -0.83664, -0.50749)0.0202, -0.0113, 0.1302
3given(-0.9473, 0.15702, 0.27921), (0.14802, -0.55844, 0.81624), (0.28409, 0.81455, 0.50577)-0.0708, -0.1729, -0.1451

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Components

#1: Protein
PROTEIN (ALDEHYDE DEHYDROGENASE) / ALDH


Mass: 54422.398 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: NAD COMPLEX / Source: (natural) Gadus callarias (Baltic cod) / Organ: LIVER / References: UniProt: P56533, betaine-aldehyde dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.59 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: 275 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 15, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→80 Å / Num. obs: 49784 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Biso Wilson estimate: 41.5 Å2 / Rsym value: 12 / Net I/σ(I): 5
Reflection shellResolution: 2.8→2.98 Å / Mean I/σ(I) obs: 1.6 / % possible all: 88.5
Reflection
*PLUS
Rmerge(I) obs: 0.124
Reflection shell
*PLUS
% possible obs: 88.5 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A4S

1a4s


Resolution: 2.8→80 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 1565193.26 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2508 5 %RANDOM
Rwork0.239 ---
obs0.239 49784 92.6 %-
Displacement parametersBiso mean: 38.1 Å2
Baniso -1Baniso -2Baniso -3
1--14.98 Å2-4.58 Å2-13.22 Å2
2--17.48 Å2-5 Å2
3----2.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 2.8→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15224 0 176 424 15824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 377 4.7 %
Rwork0.371 7567 -
obs--88.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM.NADTOPOLOGY.NAD
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Rfactor Rfree: 0.39 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.371

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