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- PDB-6jw7: The crystal structure of KanD2 in complex with NADH and 3"-deamin... -

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Basic information

Entry
Database: PDB / ID: 6jw7
TitleThe crystal structure of KanD2 in complex with NADH and 3"-deamino-3"-hydroxykanamycin A
ComponentsDehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / NAD binding
Function / homology
Function and homology information


: / GFO/IDH/MocA C-terminal domain / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-CJX / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Dehydrogenase
Similarity search - Component
Biological speciesStreptomyces kanamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsKudo, F. / Kitayama, Y. / Miyanaga, A. / Hirayama, A. / Eguchi, T.
CitationJournal: Biochemistry / Year: 2020
Title: Biochemical and structural analysis of a dehydrogenase, KanD2, and an aminotransferase, KanS2, that are responsible for the construction of the kanosamine moiety in kanamycin biosynthesis.
Authors: Kudo, F. / Kitayama, Y. / Miyanaga, A. / Hirayama, A. / Eguchi, T.
History
DepositionApr 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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 / 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
B: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0325
Polymers82,2162
Non-polymers1,8163
Water1,08160
1
A: Dehydrogenase
B: Dehydrogenase
hetero molecules

A: Dehydrogenase
B: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,06510
Polymers164,4324
Non-polymers3,6336
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area18190 Å2
ΔGint-60 kcal/mol
Surface area47660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.010, 120.010, 132.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 5 - 361 / Label seq-ID: 5 - 361

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

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Components

#1: Protein Dehydrogenase / KanD2


Mass: 41108.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces kanamyceticus (bacteria) / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6L737
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-CJX / (2R,3S,4S,5R,6R)-2-(aminomethyl)-6-[(1R,2S,3S,4R,6S)-4,6-bis(azanyl)-3-[(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-oxidanyl-cyclohexyl]oxy-oxane-3,4,5-triol / 3"-deamino-3"-hydroxykanamycin A


Mass: 485.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H35N3O12
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.33 Å3/Da / Density % sol: 63.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG 8000, imidazole, calcium acetate, NADH, 3"-deamino-3"-hydroxykanamycin A

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2018
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→50 Å / Num. obs: 45963 / % possible obs: 100 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 15.8
Reflection shellResolution: 2.36→2.49 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.996 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6640 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H3V

4h3v


Resolution: 2.36→44.57 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 14.911 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.195 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23125 2319 5 %RANDOM
Rwork0.2038 ---
obs0.2052 43605 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.231 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20.78 Å2-0 Å2
2--0.78 Å2-0 Å2
3----2.54 Å2
Refinement stepCycle: 1 / Resolution: 2.36→44.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5172 0 121 60 5353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195449
X-RAY DIFFRACTIONr_bond_other_d0.0060.025136
X-RAY DIFFRACTIONr_angle_refined_deg2.0731.9677443
X-RAY DIFFRACTIONr_angle_other_deg1.2143.00411746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4665683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38522.683246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.10715792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2081554
X-RAY DIFFRACTIONr_chiral_restr0.1160.2825
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216217
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021289
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 19756 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.36→2.421 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 191 -
Rwork0.33 3174 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3576-0.4349-0.19481.2815-0.11280.48140.05260.1219-0.0048-0.49330.020.06940.1354-0.3219-0.07260.3685-0.0857-0.040.37140.04030.017242.59-6.42518.204
20.1944-0.0262-0.01841.963-0.11230.53660.0264-0.02630.0093-0.06950.14540.28020.1596-0.2769-0.17180.1916-0.2035-0.06370.45160.12570.088230.831-26.51448.189
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 362
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2B4 - 361
4X-RAY DIFFRACTION2B401

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