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- PDB-4kue: Crystal structure of 3-hydroxybutylryl-CoA dehydrogenase from Clo... -

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Basic information

Entry
Database: PDB / ID: 4kue
TitleCrystal structure of 3-hydroxybutylryl-CoA dehydrogenase 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 / butyrate metabolic process / cellular catabolic process / 3-hydroxybutyryl-CoA dehydrogenase activity / : / 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
3-hydroxybutyryl-CoA dehydrogenase
Similarity search - Component
Biological speciesClostridium butyricum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)125,2934
Polymers125,2934
Non-polymers00
Water7,188399
1
A: 3-hydroxybutyryl-CoA dehydrogenase
B: 3-hydroxybutyryl-CoA dehydrogenase


Theoretical massNumber of molelcules
Total (without water)62,6472
Polymers62,6472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-24 kcal/mol
Surface area22930 Å2
MethodPISA
2
C: 3-hydroxybutyryl-CoA dehydrogenase
D: 3-hydroxybutyryl-CoA dehydrogenase


Theoretical massNumber of molelcules
Total (without water)62,6472
Polymers62,6472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-23 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.111, 144.111, 204.999
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
3-hydroxybutyryl-CoA dehydrogenase /


Mass: 31323.354 Da / Num. of mol.: 4 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 3.38 Å3/Da / Density % sol: 63.64 % / Mosaicity: 0.426 °
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: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97985 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97985 Å / Relative weight: 1
ReflectionRedundancy: 3.3 % / Av σ(I) over netI: 24.63 / Number: 284905 / Rmerge(I) obs: 0.057 / Χ2: 2.29 / D res high: 2 Å / D res low: 30 Å / Num. obs: 86911 / % possible obs: 81
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.423098.410.0271.2545.1
4.315.4297.210.0341.6214.7
3.764.3196.310.0593.7134.6
3.423.7695.710.085.3954.4
3.173.4293.810.0783.8554.1
2.993.1790.910.0752.4193.7
2.842.998810.0741.853.5
2.712.8486.110.081.6413.3
2.612.7184.210.0891.5383.2
2.522.6181.710.0991.5923
2.442.5280.210.1081.542.8
2.372.4477.710.1161.4912.7
2.312.3776.310.1271.5052.7
2.252.3174.210.1421.4212.5
2.22.2571.410.1541.4092.4
2.152.270.810.1631.412.3
2.112.1568.710.1711.3382.2
2.072.1166.210.1831.2722
2.032.0762.610.1951.2291.9
22.0360.210.1961.231.9
ReflectionResolution: 2→30 Å / Num. all: 107410 / Num. obs: 86911 / % possible obs: 81 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.057 / Χ2: 2.291 / Net I/σ(I): 18.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.031.90.19631961.23160.2
2.03-2.071.90.19534031.229162.6
2.07-2.1120.18335271.272166.2
2.11-2.152.20.17137071.338168.7
2.15-2.22.30.16337471.41170.8
2.2-2.252.40.15438761.409171.4
2.25-2.312.50.14239471.421174.2
2.31-2.372.70.12740631.505176.3
2.37-2.442.70.11642091.491177.7
2.44-2.522.80.10842701.54180.2
2.52-2.6130.09943951.592181.7
2.61-2.713.20.08945301.538184.2
2.71-2.843.30.0846231.641186.1
2.84-2.993.50.07447301.85188
2.99-3.173.70.07548792.419190.9
3.17-3.424.10.07849953.855193.8
3.42-3.764.40.0851515.395195.7
3.76-4.314.60.05951663.713196.3
4.31-5.424.70.03452171.621197.2
5.42-305.10.02752801.254198.4

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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
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F0Y

1f0y


Resolution: 2→29.87 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.2137 / WRfactor Rwork: 0.1692 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8367 / SU B: 4.512 / SU ML: 0.12 / SU R Cruickshank DPI: 0.1766 / SU Rfree: 0.1673 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 4395 5.1 %RANDOM
Rwork0.1866 ---
obs0.189 86911 80.92 %-
all-82516 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.24 Å2 / Biso mean: 38.2202 Å2 / Biso min: 15.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.48 Å20 Å2
2--0.48 Å2-0 Å2
3----1.56 Å2
Refinement stepCycle: LAST / Resolution: 2→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8456 0 0 399 8855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0198564
X-RAY DIFFRACTIONr_bond_other_d0.0010.028620
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.98811536
X-RAY DIFFRACTIONr_angle_other_deg0.862319924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.57851116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6825.128312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.534151632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0941540
X-RAY DIFFRACTIONr_chiral_restr0.1070.21376
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021660
X-RAY DIFFRACTIONr_mcbond_it2.9553.5744476
X-RAY DIFFRACTIONr_mcbond_other2.9533.5744475
X-RAY DIFFRACTIONr_mcangle_it3.9915.3475588
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 261 -
Rwork0.32 4503 -
all-4764 -
obs--60.3 %

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