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- PDB-3mog: Crystal structure of 3-hydroxybutyryl-CoA dehydrogenase from Esch... -

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Basic information

Entry
Database: PDB / ID: 3mog
TitleCrystal structure of 3-hydroxybutyryl-CoA dehydrogenase from Escherichia coli K12 substr. MG1655
ComponentsProbable 3-hydroxybutyryl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / NYSGRC / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


3-hydroxybutyryl-CoA dehydrogenase activity / phenylacetate catabolic process / 3-hydroxyacyl-CoA dehydrogenase activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / fatty acid metabolic process
Similarity search - Function
Transcription Regulator spoIIAA - #190 / 3-hydroxyacyl-CoA dehydrogenase PaaC / 3-hydroxybutyryl-CoA dehydrogenase reduced Rossmann-fold domain / 3-hydroxybutyryl-CoA dehydrogenase reduced Rossmann-fold domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 - #50 / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / Transcription Regulator spoIIAA / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding ...Transcription Regulator spoIIAA - #190 / 3-hydroxyacyl-CoA dehydrogenase PaaC / 3-hydroxybutyryl-CoA dehydrogenase reduced Rossmann-fold domain / 3-hydroxybutyryl-CoA dehydrogenase reduced Rossmann-fold domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 - #50 / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / Transcription Regulator spoIIAA / 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 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-hydroxyadipyl-CoA dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsPatskovsky, Y. / Ramagopal, U. / Toro, R. / Gilmore, M. / Miller, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of 3-Hydroxybutyryl-Coa Dehydrogenase from Escherichia Coli K12
Authors: Patskovsky, Y. / Ramagopal, U. / Toro, R. / Gilmore, M. / Miller, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionApr 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable 3-hydroxybutyryl-CoA dehydrogenase
B: Probable 3-hydroxybutyryl-CoA dehydrogenase
C: Probable 3-hydroxybutyryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,5628
Polymers158,2723
Non-polymers2915
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-70 kcal/mol
Surface area55530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.302, 145.753, 148.783
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable 3-hydroxybutyryl-CoA dehydrogenase / Beta-hydroxybutyryl-CoA dehydrogenase / BHBD


Mass: 52757.316 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: paaH, ydbU, b1395, JW1390 / Plasmid: BC-PSGX3(BC) / Gene (production host): PaaC-3OHAcCoADH, PAAH / Production host: Escherichia coli (E. coli) / Strain (production host): K12, MG1655
References: UniProt: P76083, 3-hydroxybutyryl-CoA dehydrogenase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 8.5
Details: 100MM TRIS-HCL, PH 8.5, 30% PEG 4K, 200MM SODIUM ACETATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 80082 / % possible obs: 99.8 % / Observed criterion σ(I): -5 / Redundancy: 5.1 % / Biso Wilson estimate: 52.32 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5 % / Mean I/σ(I) obs: 0.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SHELXmodel building
RESOLVEmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.006 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2659 2367 3 %RANDOM
Rwork0.21593 ---
obs0.21744 76421 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 69.021 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2--2.02 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10808 0 15 318 11141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211091
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.96515095
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64551429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16123.763473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.956151877
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7741590
X-RAY DIFFRACTIONr_chiral_restr0.0840.21771
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218314
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.14227048
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.711311344
X-RAY DIFFRACTIONr_scbond_it5.72834043
X-RAY DIFFRACTIONr_scangle_it7.82753741
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 159 -
Rwork0.328 5388 -
obs--97.06 %

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