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- PDB-5ojg: Crystal structure of the dehydrogenase/reductase SDR family membe... -

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Basic information

Entry
Database: PDB / ID: 5ojg
TitleCrystal structure of the dehydrogenase/reductase SDR family member 4 (DHRS4) from Caenorhabditis elegans
ComponentsDehydrogenase/reductase SDR family member 4
KeywordsOXIDOREDUCTASE / dehydrogenase SDR biotransformation
Function / homology
Function and homology information


RA biosynthesis pathway / Peroxisomal protein import / carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / catalytic activity
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / 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
butane-2,3-dione / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dehydrogenase/reductase SDR family member 4
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsScheidig, A.J. / Faust, A. / Ebert, B. / Maser, E. / Kisiela, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationMA 1704/12-1 Germany
CitationJournal: FEBS J. / Year: 2018
Title: Crystal structure and catalytic characterization of the dehydrogenase/reductase SDR family member 4 (DHRS4) from Caenorhabditis elegans.
Authors: Kisiela, M. / Faust, A. / Ebert, B. / Maser, E. / Scheidig, A.J.
History
DepositionJul 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Jan 17, 2024Group: 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dehydrogenase/reductase SDR family member 4
B: Dehydrogenase/reductase SDR family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9046
Polymers55,2452
Non-polymers1,6594
Water9,170509
1
A: Dehydrogenase/reductase SDR family member 4
B: Dehydrogenase/reductase SDR family member 4
hetero molecules

A: Dehydrogenase/reductase SDR family member 4
B: Dehydrogenase/reductase SDR family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,80912
Polymers110,4914
Non-polymers3,3188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area19580 Å2
ΔGint-94 kcal/mol
Surface area33560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.600, 93.600, 132.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 260 / Label seq-ID: 1 - 260

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Dehydrogenase/reductase SDR family member 4


Mass: 27622.740 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: dhrs-4, F54F3.4 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G5EGA6, carbonyl reductase (NADPH)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-BUO / butane-2,3-dione


Mass: 86.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 10 % (w/v) PEG 8000 200 mM NaCl 100 mM K/Na-phospate pH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976261 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976261 Å / Relative weight: 1
ReflectionResolution: 1.9→76.35 Å / Num. obs: 46906 / % possible obs: 99.9 % / Redundancy: 23.3 % / CC1/2: 0.995 / Rpim(I) all: 0.489 / Net I/σ(I): 8.3
Reflection shellResolution: 1.9→1.95 Å / Num. unique obs: 3280 / CC1/2: 0.214 / Rpim(I) all: 5.039 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O4R

3o4r


Resolution: 1.9→76.35 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.331 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22344 2346 5 %RANDOM
Rwork0.17911 ---
obs0.18133 44560 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.408 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å2-0 Å2-0 Å2
2--0.71 Å2-0 Å2
3----1.42 Å2
Refinement stepCycle: 1 / Resolution: 1.9→76.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 108 509 4497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194084
X-RAY DIFFRACTIONr_bond_other_d0.0020.024007
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.9945542
X-RAY DIFFRACTIONr_angle_other_deg1.0192.9999215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8385524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57325.097155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7915701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0451517
X-RAY DIFFRACTIONr_chiral_restr0.1010.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024603
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02874
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_it3.023.2282087
X-RAY DIFFRACTIONr_mcbond_other3.0183.2272086
X-RAY DIFFRACTIONr_mcangle_it4.5254.8272608
X-RAY DIFFRACTIONr_mcangle_other4.5254.8282609
X-RAY DIFFRACTIONr_scbond_it4.0753.6971997
X-RAY DIFFRACTIONr_scbond_other4.0753.6981998
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1035.3542932
X-RAY DIFFRACTIONr_long_range_B_refined8.72841.6564972
X-RAY DIFFRACTIONr_long_range_B_other8.58640.9214812
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 16248 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 173 -
Rwork0.367 3280 -
obs--99.97 %

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