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- PDB-6g1m: Amine Dehydrogenase from Petrotoga mobilis; open and closed form -

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Basic information

Entry
Database: PDB / ID: 6g1m
TitleAmine Dehydrogenase from Petrotoga mobilis; open and closed form
ComponentsDihydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / Amine Dehydrogenase / reductive aminase / NADH
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate reductase / lysine biosynthetic process via diaminopimelate / nucleotide binding
Similarity search - Function
2,4-diaminopentanoate dehydrogenase, C-terminal domain / 2,4-diaminopentanoate dehydrogenase C-terminal domain / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Dihydrodipicolinate reductase
Similarity search - Component
Biological speciesPetrotoga mobilis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsBeloti, L. / Frese, A. / Mayol, O. / Vaxelaire-Vergne, C. / Grogan, G.
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
DepositionMar 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
B: Dihydrodipicolinate reductase
C: Dihydrodipicolinate reductase
D: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,22210
Polymers147,3794
Non-polymers2,8446
Water4,864270
1
A: Dihydrodipicolinate reductase
B: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1115
Polymers73,6892
Non-polymers1,4223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-47 kcal/mol
Surface area24210 Å2
MethodPISA
2
C: Dihydrodipicolinate reductase
D: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1115
Polymers73,6892
Non-polymers1,4223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-47 kcal/mol
Surface area24450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.113, 83.642, 125.712
Angle α, β, γ (deg.)90.00, 94.28, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-561-

HOH

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: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 335 / Label seq-ID: 1 - 335

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Dihydrodipicolinate reductase


Mass: 36844.691 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petrotoga mobilis (strain DSM 10674 / SJ95) (bacteria)
Strain: DSM 10674 / SJ95 / Gene: Pmob_1166 / Production host: Escherichia coli (E. coli) / References: UniProt: A9BHL2
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl pH 6.5, 0,2M Li2SO4, 25% PEG 2000 MME

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97965 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97965 Å / Relative weight: 1
ReflectionResolution: 2.32→125.36 Å / Num. obs: 62492 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 32 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.08 / Net I/σ(I): 9.6
Reflection shellResolution: 2.32→2.38 Å / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4560 / CC1/2: 0.82 / Rpim(I) all: 0.43 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G1H

6g1h


Resolution: 2.32→125.36 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.871 / SU B: 9.088 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.437 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29531 3155 5 %RANDOM
Rwork0.24808 ---
obs0.25044 59332 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.936 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0 Å2-1.17 Å2
2---0.12 Å2-0 Å2
3---1.09 Å2
Refinement stepCycle: 1 / Resolution: 2.32→125.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9768 0 186 270 10224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01910144
X-RAY DIFFRACTIONr_bond_other_d0.0020.029490
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.9913865
X-RAY DIFFRACTIONr_angle_other_deg1.09321953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44651328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.44425.689341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.569151581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7741524
X-RAY DIFFRACTIONr_chiral_restr0.1150.21692
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111141
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021795
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_it2.7083.4755333
X-RAY DIFFRACTIONr_mcbond_other2.7043.4745332
X-RAY DIFFRACTIONr_mcangle_it4.0285.2056654
X-RAY DIFFRACTIONr_mcangle_other4.0295.2056655
X-RAY DIFFRACTIONr_scbond_it2.893.6514811
X-RAY DIFFRACTIONr_scbond_other2.8783.6494804
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2725.3997200
X-RAY DIFFRACTIONr_long_range_B_refined5.94741.67910560
X-RAY DIFFRACTIONr_long_range_B_other5.94741.67710561
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)
11A186080.1
12B186080.1
21A188340.11
22C188340.11
31A199380.04
32D199380.04
41B200680.06
42C200680.06
51B187540.1
52D187540.1
61C189600.1
62D189600.1
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 238 -
Rwork0.297 4320 -
obs--99.11 %

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