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- PDB-2yz7: X-ray analyses of 3-hydroxybutyrate dehydrogenase from Alcaligene... -

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Basic information

Entry
Database: PDB / ID: 2yz7
TitleX-ray analyses of 3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis
ComponentsD-3-hydroxybutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / 3-hydroxybutyrate dehydrogenase
Function / homology
Function and homology information


3-hydroxybutyrate dehydrogenase / 3-hydroxybutyrate dehydrogenase activity / nucleotide binding / metal ion binding
Similarity search - Function
3-hydroxybutyrate dehydrogenase / : / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-hydroxybutyrate dehydrogenase
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsHoque, M.M. / Juan, E.C.M. / Shimizu, S. / Hossain, M.T. / Takenaka, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: The structures of Alcaligenes faecalisD-3-hydroxybutyrate dehydrogenase before and after NAD(+) and acetate binding suggest a dynamical reaction mechanism as a member of the SDR family.
Authors: Hoque, M.M. / Shimizu, S. / Hossain, M.T. / Yamamoto, T. / Imamura, S. / Suzuki, K. / Tsunoda, M. / Amano, H. / Sekiguchi, T. / Takenaka, A.
History
DepositionMay 4, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: D-3-hydroxybutyrate dehydrogenase
B: D-3-hydroxybutyrate dehydrogenase
C: D-3-hydroxybutyrate dehydrogenase
D: D-3-hydroxybutyrate dehydrogenase
E: D-3-hydroxybutyrate dehydrogenase
F: D-3-hydroxybutyrate dehydrogenase
G: D-3-hydroxybutyrate dehydrogenase
H: D-3-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,39520
Polymers216,9528
Non-polymers44412
Water7,206400
1
A: D-3-hydroxybutyrate dehydrogenase
B: D-3-hydroxybutyrate dehydrogenase
C: D-3-hydroxybutyrate dehydrogenase
D: D-3-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,69810
Polymers108,4764
Non-polymers2226
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12540 Å2
ΔGint-153.7 kcal/mol
Surface area35860 Å2
MethodPISA
2
E: D-3-hydroxybutyrate dehydrogenase
F: D-3-hydroxybutyrate dehydrogenase
G: D-3-hydroxybutyrate dehydrogenase
H: D-3-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,69810
Polymers108,4764
Non-polymers2226
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12440 Å2
ΔGint-157.6 kcal/mol
Surface area35860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.302, 118.827, 118.726
Angle α, β, γ (deg.)90.00, 93.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
D-3-hydroxybutyrate dehydrogenase


Mass: 27118.943 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria)
References: UniProt: D0VWQ0*PLUS, 3-hydroxybutyrate dehydrogenase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN UNIPROT PROTEIN SEQUENCE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN UNIPROT PROTEIN SEQUENCE DATABASE. THIS SEQUENCE WILL BE DEPOSITED IN UNIPROT.

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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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 28% PEG 4000, 0.1M lithium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 15, 2004
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 102135 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.076
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.34 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HSD

2hsd


Resolution: 2.19→50 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.27 6107 5.6 %Random
Rwork0.197 ---
obs-60246 54.8 %-
Solvent computationBsol: 47.474 Å2
Displacement parametersBiso mean: 45.018 Å2
Baniso -1Baniso -2Baniso -3
1--12.899 Å20 Å2-10.392 Å2
2--6.014 Å20 Å2
3---6.886 Å2
Refinement stepCycle: LAST / Resolution: 2.19→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15248 0 12 400 15660
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1921.5
X-RAY DIFFRACTIONc_scbond_it1.7682
X-RAY DIFFRACTIONc_mcangle_it1.9222
X-RAY DIFFRACTIONc_scangle_it2.5552.5

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