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- PDB-6jw6: The crystal structure of KanD2 in complex with NAD -

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Basic information

Entry
Database: PDB / ID: 6jw6
TitleThe crystal structure of KanD2 in complex with NAD
ComponentsDehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / NAD binding
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
: / : / 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 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Dehydrogenase
Similarity search - Component
Biological speciesStreptomyces kanamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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

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Assembly

Deposited unit
A: Dehydrogenase
B: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5434
Polymers82,2162
Non-polymers1,3272
Water1448
1
A: Dehydrogenase
B: Dehydrogenase
hetero molecules

A: Dehydrogenase
B: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,0868
Polymers164,4324
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area17900 Å2
ΔGint-57 kcal/mol
Surface area48280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.469, 119.469, 131.435
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: PRO / Beg label comp-ID: PRO / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 4 - 361 / Label seq-ID: 4 - 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, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.39 Å3/Da / Density % sol: 63.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 8000, imidazole, calcium acetate, NAD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 27212 / % possible obs: 100 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 23.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.918 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3916 / % 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: 2.8→48.18 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 26.569 / SU ML: 0.231 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.595 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 1353 5 %RANDOM
Rwork0.1962 ---
obs0.1985 25759 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 176.51 Å2 / Biso mean: 79.263 Å2 / Biso min: 44.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.34 Å2-0 Å2
2---0.34 Å2-0 Å2
3---1.11 Å2
Refinement stepCycle: final / Resolution: 2.8→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5168 0 88 8 5264
Biso mean--79.77 61.01 -
Num. residues----682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195398
X-RAY DIFFRACTIONr_bond_other_d0.0050.025087
X-RAY DIFFRACTIONr_angle_refined_deg1.681.967369
X-RAY DIFFRACTIONr_angle_other_deg1.04311625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5845680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47622.735245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.43115789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5311553
X-RAY DIFFRACTIONr_chiral_restr0.090.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216191
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021284
Refine LS restraints NCS

Ens-ID: 1 / Number: 20175 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 111 -
Rwork0.321 1874 -
all-1985 -
obs--99.85 %
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)
10.2326-0.39620.18511.09580.09520.63340.08330.0244-0.0426-0.38560.02950.0074-0.17330.2603-0.11280.4043-0.05720.0640.342-0.05250.125-42.0656.28717.675
20.02540.11060.04311.46150.17220.4530.033-0.0331-0.034-0.1040.1543-0.142-0.15190.2485-0.18730.2264-0.3190.10770.4541-0.15220.1991-30.55426.54447.648
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 361
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION1A501 - 506
4X-RAY DIFFRACTION2B4 - 361
5X-RAY DIFFRACTION2B401
6X-RAY DIFFRACTION2B501 - 502

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