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- PDB-6iaq: Structure of Amine Dehydrogenase from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 6iaq
TitleStructure of Amine Dehydrogenase from Mycobacterium smegmatis
ComponentsDihydrodipicolinate reductase N-terminus domain-containing protein
KeywordsOXIDOREDUCTASE / Amine Dehydrogenase / NADP / biocatalysis / amine
Function / homology2,4-diaminopentanoate dehydrogenase C-terminal domain / 4-hydroxy-tetrahydrodipicolinate reductase / 4-hydroxy-tetrahydrodipicolinate reductase / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / lysine biosynthetic process via diaminopimelate / NAD(P)-binding domain superfamily / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrodipicolinate reductase N-terminus domain-containing protein
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsGrogan, G. / Vaxelaire-Vergne, C. / Beloti, L. / Mayol, O.
CitationJournal: Nat Catal / Year: 2019
Title: A family of native amine dehydrogenases for the asymmetric reductive amination of ketones
Authors: Mayol, O. / Bastard, K. / Beloti, L. / Frese, A. / Turkenburg, J.P. / Petit, J.-L. / Mariage, A. / Debard, A. / Pellouin, V. / Perret, A. / de Berardinis, V. / Zaparucha, A. / Grogan, G. / Vaxelaire-Vergne, C.
History
DepositionNov 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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: Dihydrodipicolinate reductase N-terminus domain-containing protein
B: Dihydrodipicolinate reductase N-terminus domain-containing protein
C: Dihydrodipicolinate reductase N-terminus domain-containing protein
D: Dihydrodipicolinate reductase N-terminus domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,17312
Polymers145,9524
Non-polymers3,2228
Water12,034668
1
A: Dihydrodipicolinate reductase N-terminus domain-containing protein
C: Dihydrodipicolinate reductase N-terminus domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5876
Polymers72,9762
Non-polymers1,6114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-23 kcal/mol
Surface area24140 Å2
MethodPISA
2
B: Dihydrodipicolinate reductase N-terminus domain-containing protein
D: Dihydrodipicolinate reductase N-terminus domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5876
Polymers72,9762
Non-polymers1,6114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-23 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.390, 147.910, 97.780
Angle α, β, γ (deg.)90.00, 98.18, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 3344 - 338
21BB0 - 3344 - 338
12AA1 - 3345 - 338
22CC1 - 3345 - 338
13AA-2 - 3342 - 338
23DD-2 - 3342 - 338
14BB1 - 3345 - 338
24CC1 - 3345 - 338
15BB0 - 3344 - 338
25DD0 - 3344 - 338
16CC1 - 3345 - 338
26DD1 - 3345 - 338

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Dihydrodipicolinate reductase N-terminus domain-containing protein


Mass: 36487.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: dapB_2, ERS451418_03299 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: A0A0D6I8P6, 4-hydroxy-tetrahydrodipicolinate reductase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 0.1 M bis-Tris pH 6.5; 0.2 M Magnesium Chloride; 10 mM NADP+

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.91→49.3 Å / Num. obs: 110014 / % possible obs: 98.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 32 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.04 / Net I/σ(I): 12.5
Reflection shellResolution: 1.91→1.94 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5416 / CC1/2: 0.69 / Rpim(I) all: 0.6 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GET

6get
PDB Unreleased entry


Resolution: 1.91→48.15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.629 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.147 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 5436 4.9 %RANDOM
Rwork0.20038 ---
obs0.20197 104537 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.863 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å2-2.46 Å2
2---0.36 Å20 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.91→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10016 0 208 668 10892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01310419
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179538
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.67214267
X-RAY DIFFRACTIONr_angle_other_deg1.391.58322030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76751344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4722.525491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.184151551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2481568
X-RAY DIFFRACTIONr_chiral_restr0.0760.21447
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211770
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022094
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_it3.1383.7665388
X-RAY DIFFRACTIONr_mcbond_other3.1373.7665387
X-RAY DIFFRACTIONr_mcangle_it4.1035.6396728
X-RAY DIFFRACTIONr_mcangle_other4.1035.6396729
X-RAY DIFFRACTIONr_scbond_it3.5293.9645031
X-RAY DIFFRACTIONr_scbond_other3.5293.9635032
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0245.8457540
X-RAY DIFFRACTIONr_long_range_B_refined6.34444.77411370
X-RAY DIFFRACTIONr_long_range_B_other6.32544.61811254
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A101610.07
12B101610.07
21A101530.07
22C101530.07
31A102850.05
32D102850.05
41B101680.07
42C101680.07
51B101520.06
52D101520.06
61C100830.07
62D100830.07
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 407 -
Rwork0.318 7699 -
obs--98.36 %

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