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- PDB-4tkm: Crystal structure of NADH-dependent reductase A1-R' complexed with NAD -

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Basic information

Entry
Database: PDB / ID: 4tkm
TitleCrystal structure of NADH-dependent reductase A1-R' complexed with NAD
ComponentsNADH-dependent reductase for 4-deoxy-L-erythro-5-hexoseulose uronate
KeywordsOXIDOREDUCTASE / ALPHA/BETA/ALPHA / ROSSMANN-FOLD / Alginate metabolism / Short-chain dehydrogenase/reductase
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / quinone binding / fatty acid biosynthetic process / nucleotide binding
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADH-dependent reductase for 4-deoxy-L-erythro-5-hexoseulose uronate
Similarity search - Component
Biological speciesSphingomonas sp. A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 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
DepositionMay 27, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Jan 22, 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

Downloads & links

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Assembly

Deposited unit
A: NADH-dependent reductase for 4-deoxy-L-erythro-5-hexoseulose uronate
B: NADH-dependent reductase for 4-deoxy-L-erythro-5-hexoseulose uronate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8828
Polymers54,7382
Non-polymers1,1446
Water1,45981
1
A: NADH-dependent reductase for 4-deoxy-L-erythro-5-hexoseulose uronate
B: NADH-dependent reductase for 4-deoxy-L-erythro-5-hexoseulose uronate
hetero molecules

A: NADH-dependent reductase for 4-deoxy-L-erythro-5-hexoseulose uronate
B: NADH-dependent reductase for 4-deoxy-L-erythro-5-hexoseulose uronate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,76416
Polymers109,4764
Non-polymers2,28712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area16950 Å2
ΔGint-206 kcal/mol
Surface area31010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.898, 87.898, 139.821
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

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Components

#1: Protein NADH-dependent reductase for 4-deoxy-L-erythro-5-hexoseulose uronate


Mass: 27369.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. A1 (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A075B5H4*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 400, Ammonium sulphate, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, NAD

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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: Oct 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.67→33.5 Å / Num. obs: 18404 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 43.4
Reflection shellResolution: 2.67→2.77 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data processing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AFM

3afm


Resolution: 2.67→33.45 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.906 / SU B: 11.683 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.651 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27801 938 5.1 %RANDOM
Rwork0.19516 ---
obs0.19916 17397 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å21.32 Å20 Å2
2--1.32 Å20 Å2
3----4.29 Å2
Refinement stepCycle: 1 / Resolution: 2.67→33.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3581 0 69 81 3731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193711
X-RAY DIFFRACTIONr_bond_other_d0.0010.023537
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.9695025
X-RAY DIFFRACTIONr_angle_other_deg0.78238090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6325479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91623.067150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1715581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1331528
X-RAY DIFFRACTIONr_chiral_restr0.0730.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024234
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02871
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_it2.9724.8551928
X-RAY DIFFRACTIONr_mcbond_other2.9714.8561927
X-RAY DIFFRACTIONr_mcangle_it4.5637.2722403
X-RAY DIFFRACTIONr_mcangle_other4.5627.2722404
X-RAY DIFFRACTIONr_scbond_it2.9675.2441783
X-RAY DIFFRACTIONr_scbond_other2.8715.1621764
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5967.6512592
X-RAY DIFFRACTIONr_long_range_B_refined12.04739.4024380
X-RAY DIFFRACTIONr_long_range_B_other12.04639.4114381
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.665→2.734 Å / Rfactor Rfree error: 0.35
RfactorNum. reflection% reflection
Rfree0.368 71 -
Rwork0.264 1231 -
obs--99.39 %

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