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- PDB-4w7h: Crystal Structure of DEH Reductase A1-R Mutant -

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Basic information

Entry
Database: PDB / ID: 4w7h
TitleCrystal Structure of DEH Reductase A1-R Mutant
ComponentsCarbonyl reductase
KeywordsOXIDOREDUCTASE / ALPHA/BETA/ALPHA / ROSSMANN-FOLD / Alginate metabolism / Short-chain dehydrogenase/reductase / loop-exchange
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
: / PKS_KR / 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
Biological speciesSphingomonas sp. A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsTakase, R. / Mikami, B. / Kawai, S. / Murata, K. / Hashimoto, W.
Funding support Japan, 4items
OrganizationGrant numberCountry
Grants-in-Aid for Scientific Research from Japan Society for the Promotion of Science Japan
Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN) of Japan Japan
Targeted Proteins Research Program from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan Japan
Research fellowships from Japan Society for the Promotion of Science for Young Scientists Japan
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure-based Conversion of the Coenzyme Requirement of a Short-chain Dehydrogenase/Reductase Involved in Bacterial Alginate Metabolism.
Authors: Takase, R. / Mikami, B. / Kawai, S. / Murata, K. / Hashimoto, W.
History
DepositionAug 22, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Jan 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonyl reductase
B: Carbonyl reductase


Theoretical massNumber of molelcules
Total (without water)53,9932
Polymers53,9932
Non-polymers00
Water1267
1
A: Carbonyl reductase
B: Carbonyl reductase

A: Carbonyl reductase
B: Carbonyl reductase


Theoretical massNumber of molelcules
Total (without water)107,9864
Polymers107,9864
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area12830 Å2
ΔGint-80 kcal/mol
Surface area32050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.500, 104.500, 68.116
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Carbonyl reductase / 4-deoxy-L-erythro-5-hexoseulose uronate reductase A1-R


Mass: 26996.434 Da / Num. of mol.: 2 / Mutation: S16T/Q17E/H37N/G38S/R39H/K40V/A41D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. A1 (bacteria) / Gene: a1-R / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6RU56
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.99 Å3/Da / Density % sol: 38.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: PEG 4000, Lithium chloride, tris (hydroxymethyl) aminomethane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.11→50 Å / Num. obs: 7885 / % possible obs: 99.5 % / Redundancy: 11.3 % / Net I/σ(I): 67.5

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AFM

3afm


Resolution: 3.11→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.876 / SU B: 27.451 / SU ML: 0.485 / Cross valid method: THROUGHOUT / ESU R Free: 0.661 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29465 361 4.7 %RANDOM
Rwork0.19725 ---
obs0.20177 7336 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.512 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.16 Å20 Å2
2--0.31 Å20 Å2
3----1.02 Å2
Refinement stepCycle: 1 / Resolution: 3.11→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3598 0 0 7 3605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193670
X-RAY DIFFRACTIONr_bond_other_d0.0010.023494
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.944967
X-RAY DIFFRACTIONr_angle_other_deg0.738008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0595487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.523.907151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58915555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3331518
X-RAY DIFFRACTIONr_chiral_restr0.0540.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214275
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02859
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_it3.0047.7541960
X-RAY DIFFRACTIONr_mcbond_other3.0047.7541959
X-RAY DIFFRACTIONr_mcangle_it4.9111.612443
X-RAY DIFFRACTIONr_mcangle_other4.90911.6112444
X-RAY DIFFRACTIONr_scbond_it2.5618.0111709
X-RAY DIFFRACTIONr_scbond_other2.568.0111710
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2411.9032524
X-RAY DIFFRACTIONr_long_range_B_refined7.28262.0574154
X-RAY DIFFRACTIONr_long_range_B_other7.28262.0624155
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.11→3.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 20 -
Rwork0.32 523 -
obs--95.6 %

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