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- PDB-4pzd: Crystal structure of (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1... -

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Basic information

Entry
Database: PDB / ID: 4pzd
TitleCrystal structure of (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 in complex with NAD+
Components3-Hydroxyacyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann Fold
Function / homology
Function and homology information


3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / catabolic process / NAD+ binding / fatty acid metabolic process
Similarity search - Function
3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 ...3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-Hydroxyacyl-CoA dehydrogenase
Similarity search - Component
Biological speciesRalstonia eutropha H16 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.61 Å
AuthorsKim, J. / Chang, J.H. / Kim, K.J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystal structure and biochemical properties of the (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 from Ralstonia eutropha
Authors: Kim, J. / Chang, J.H. / Kim, K.J.
History
DepositionMar 29, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Derived calculations
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: 3-Hydroxyacyl-CoA dehydrogenase
B: 3-Hydroxyacyl-CoA dehydrogenase
C: 3-Hydroxyacyl-CoA dehydrogenase
D: 3-Hydroxyacyl-CoA dehydrogenase
E: 3-Hydroxyacyl-CoA dehydrogenase
F: 3-Hydroxyacyl-CoA dehydrogenase
G: 3-Hydroxyacyl-CoA dehydrogenase
H: 3-Hydroxyacyl-CoA dehydrogenase
I: 3-Hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,30518
Polymers272,3349
Non-polymers5,9719
Water1,820101
1
A: 3-Hydroxyacyl-CoA dehydrogenase
hetero molecules

A: 3-Hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8454
Polymers60,5192
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area3720 Å2
ΔGint-27 kcal/mol
Surface area24580 Å2
MethodPISA
2
B: 3-Hydroxyacyl-CoA dehydrogenase
C: 3-Hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8454
Polymers60,5192
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-26 kcal/mol
Surface area23580 Å2
MethodPISA
3
D: 3-Hydroxyacyl-CoA dehydrogenase
G: 3-Hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8454
Polymers60,5192
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-25 kcal/mol
Surface area24410 Å2
MethodPISA
4
E: 3-Hydroxyacyl-CoA dehydrogenase
F: 3-Hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8454
Polymers60,5192
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-27 kcal/mol
Surface area23490 Å2
MethodPISA
5
H: 3-Hydroxyacyl-CoA dehydrogenase
I: 3-Hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8454
Polymers60,5192
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-27 kcal/mol
Surface area23480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.076, 135.586, 97.445
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
3-Hydroxyacyl-CoA dehydrogenase


Mass: 30259.309 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha H16 (bacteria) / Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: paaH1, H16_A0282 / Production host: Escherichia coli (E. coli)
References: UniProt: Q0KEY8, 3-hydroxyacyl-CoA dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M (NH4)2SO4, 0.1M Cacodylate pH 6.5, 0.2M Sodium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 16, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 91442
Reflection shellResolution: 2.6→2.69 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.61→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.904 / SU B: 12.043 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.77 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26861 4557 5 %RANDOM
Rwork0.19901 ---
obs0.20246 86885 98.64 %-
all-88082 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.31 Å2
Baniso -1Baniso -2Baniso -3
1-3.76 Å2-0 Å2-0.06 Å2
2--3.56 Å2-0 Å2
3----7.32 Å2
Refinement stepCycle: LAST / Resolution: 2.61→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18918 0 396 101 19415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01919584
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219521
X-RAY DIFFRACTIONr_angle_refined_deg1.6862.01226568
X-RAY DIFFRACTIONr_angle_other_deg0.846344955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77952538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.01624.658657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.682153465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6221599
X-RAY DIFFRACTIONr_chiral_restr0.0840.23240
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0221600
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023906
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7046.58510179
X-RAY DIFFRACTIONr_mcbond_other4.7046.58410178
X-RAY DIFFRACTIONr_mcangle_it6.9089.86212708
X-RAY DIFFRACTIONr_mcangle_other6.9089.86212709
X-RAY DIFFRACTIONr_scbond_it5.097.1699405
X-RAY DIFFRACTIONr_scbond_other5.0897.1699406
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.67410.58513861
X-RAY DIFFRACTIONr_long_range_B_refined10.79253.15122235
X-RAY DIFFRACTIONr_long_range_B_other10.79253.15222236
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.611→2.678 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 313 -
Rwork0.275 6195 -
obs--96.1 %

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