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- PDB-4kuh: Crystal structure of 3-hydroxybutylryl-CoA dehydrogenase with ace... -

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Basic information

Entry
Database: PDB / ID: 4kuh
TitleCrystal structure of 3-hydroxybutylryl-CoA dehydrogenase with acetoacetyl-CoA from Clostridium butyricum
Components3-hydroxybutyryl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / HCDH C-domain-like/NAD(P)-binding protein / beta-hydroxyacyl-CoA dehydrogenase activity
Function / homology
Function and homology information


3-hydroxybutyryl-CoA dehydrogenase / 3-hydroxybutyryl-CoA dehydrogenase activity / butyrate metabolic process / cellular catabolic process / organic substance catabolic process / NAD+ binding
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 / 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
ACETOACETYL-COENZYME A / 3-hydroxybutyryl-CoA dehydrogenase
Similarity search - Component
Biological speciesClostridium butyricum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å
AuthorsKim, E.J. / Kim, S. / Kim, K.J.
CitationJournal: to be published
Title: Crystal structure of (S)-3-hydroxybutylryl-CoA dehydrogenase form the n-butanol sysnthesizing bacterium, Clostridium butyricum
Authors: Kim, E.J. / Kim, S. / Kim, K.J.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)253,11513
Polymers248,8578
Non-polymers4,2585
Water2,774154
1
A: 3-hydroxybutyryl-CoA dehydrogenase
B: 3-hydroxybutyryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0663
Polymers62,2142
Non-polymers8521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-18 kcal/mol
Surface area23110 Å2
MethodPISA
2
C: 3-hydroxybutyryl-CoA dehydrogenase
D: 3-hydroxybutyryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0663
Polymers62,2142
Non-polymers8521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-16 kcal/mol
Surface area23060 Å2
MethodPISA
3
E: 3-hydroxybutyryl-CoA dehydrogenase
F: 3-hydroxybutyryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9174
Polymers62,2142
Non-polymers1,7032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-16 kcal/mol
Surface area23380 Å2
MethodPISA
4
G: 3-hydroxybutyryl-CoA dehydrogenase
H: 3-hydroxybutyryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0663
Polymers62,2142
Non-polymers8521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-16 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.338, 146.338, 409.757
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11F-409-

HOH

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Components

#1: Protein
3-hydroxybutyryl-CoA dehydrogenase /


Mass: 31107.094 Da / Num. of mol.: 8 / Fragment: UNP residues 1-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium butyricum (bacteria) / Strain: E4 str. BoNT E BL5262 / Gene: hbd, CLP_3850 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: C4IEM5, 3-hydroxybutyryl-CoA dehydrogenase
#2: Chemical
ChemComp-CAA / ACETOACETYL-COENZYME A / Acetoacetyl-CoA


Mass: 851.607 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 3.49 Å3/Da / Density % sol: 64.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: (NH4)2SO4, CAPs, Li2SO4, pH 10.5, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.6 % / Av σ(I) over netI: 15.33 / Number: 374966 / Rmerge(I) obs: 0.088 / Χ2: 2.31 / D res high: 2.5 Å / D res low: 30 Å / Num. obs: 103800 / % possible obs: 92.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.52.5481.210.3060.9142.2
2.542.5982.910.2991.0432.3
2.592.6484.810.2870.9372.4
2.642.6985.210.2810.9382.5
2.692.7587.410.2631.0062.6
2.752.8288.610.2491.1452.7
2.822.8988.510.2331.1222.8
2.892.9690.710.2091.2473
2.963.0592.110.2031.3933.1
3.053.1593.110.1821.4713.3
3.153.2694.410.1491.7443.5
3.263.3995.810.1381.9673.8
3.393.5596.310.1182.3764
3.553.7397.710.1062.6474.2
3.733.9797.710.0993.3344.4
3.974.2798.310.0944.2534.6
4.274.798.410.0854.2854.8
4.75.3898.810.0712.9744.7
5.386.7699.410.062.044.8
6.763099.810.0412.0945.5
ReflectionResolution: 2.5→30 Å / Num. all: 112292 / Num. obs: 103800 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.5-2.542.20.306181.2
2.54-2.592.30.299182.9
2.59-2.642.40.287184.8
2.64-2.692.50.281185.2
2.69-2.752.60.263187.4
2.75-2.822.70.249188.6
2.82-2.892.80.233188.5
2.89-2.9630.209190.7
2.96-3.053.10.203192.1
3.05-3.153.30.182193.1
3.15-3.263.50.149194.4
3.26-3.393.80.138195.8
3.39-3.5540.118196.3
3.55-3.734.20.106197.7
3.73-3.974.40.099197.7
3.97-4.274.60.094198.3
4.27-4.74.80.085198.4
4.7-5.384.70.071198.8
5.38-6.764.80.06199.4
6.76-305.50.041199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→29.55 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 10.337 / SU ML: 0.22 / SU R Cruickshank DPI: 0.3896 / Cross valid method: THROUGHOUT / ESU R: 0.385 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25738 5229 5 %RANDOM
Rwork0.19093 ---
obs0.19427 98569 92.44 %-
all-98571 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.767 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.23 Å2-0 Å2
2--0.23 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.51→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16912 0 270 154 17336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01917400
X-RAY DIFFRACTIONr_bond_other_d0.0010.0217410
X-RAY DIFFRACTIONr_angle_refined_deg1.6492.00423471
X-RAY DIFFRACTIONr_angle_other_deg0.807340243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.28652232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.34925.128624
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.824153264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5941580
X-RAY DIFFRACTIONr_chiral_restr0.0790.22782
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219079
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023370
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_it3.5725.0728952
X-RAY DIFFRACTIONr_mcbond_other3.5725.0728951
X-RAY DIFFRACTIONr_mcangle_it5.3037.59911176
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1895.7158448
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.51→2.572 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 362 -
Rwork0.337 6282 -
obs--80.62 %

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