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- PDB-6iau: Amine Dehydrogenase from Cystobacter fuscus in complex with NADP+... -

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Basic information

Entry
Database: PDB / ID: 6iau
TitleAmine Dehydrogenase from Cystobacter fuscus in complex with NADP+ and cyclohexylamine
ComponentsAmine Dehydrogenase
KeywordsOXIDOREDUCTASE / Amine / NADP / Dehydrogenase
Function / homology2,4-diaminopentanoate dehydrogenase, C-terminal domain / 2,4-diaminopentanoate dehydrogenase C-terminal domain / NAD(P)-binding domain superfamily / nucleotide binding / CYCLOHEXYLAMMONIUM ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2,4-diaminopentanoate dehydrogenase C-terminal domain-containing protein
Function and homology information
Biological speciesCystobacter fuscus DSM 2262 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBeloti, L. / Mayol, O. / Turkenburg, J.P. / 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
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: Amine Dehydrogenase
B: Amine Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6564
Polymers74,8122
Non-polymers8442
Water4,684260
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-22 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.000, 87.000, 143.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 3 - 340 / Label seq-ID: 7 - 344

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

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Components

#1: Protein Amine Dehydrogenase


Mass: 37406.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cystobacter fuscus DSM 2262 (bacteria) / Gene: D187_009359 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: S9Q235
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-HAI / CYCLOHEXYLAMMONIUM ION


Mass: 100.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.14 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.0 M ammonium sulfate, 0.1 M Tris-HCl pH 8.5; 10 mM NADP+; 20 mM cyclohexylamine

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.97→55.24 Å / Num. obs: 45901 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 19 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.08 / Net I/σ(I): 9.2
Reflection shellResolution: 1.97→2.02 Å / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3174 / CC1/2: 0.85 / Rpim(I) all: 0.43

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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: 1.97→55.24 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.59 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21734 2265 4.9 %RANDOM
Rwork0.19008 ---
obs0.19144 43558 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.738 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å20 Å2
2--4.12 Å2-0 Å2
3----2.36 Å2
Refinement stepCycle: 1 / Resolution: 1.97→55.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5055 0 55 260 5370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135218
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174767
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.6587144
X-RAY DIFFRACTIONr_angle_other_deg1.4521.57410979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1685678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30521.155251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1515757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1051541
X-RAY DIFFRACTIONr_chiral_restr0.090.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025939
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021101
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_it2.2132.7072718
X-RAY DIFFRACTIONr_mcbond_other2.2122.7062717
X-RAY DIFFRACTIONr_mcangle_it3.2074.053394
X-RAY DIFFRACTIONr_mcangle_other3.2074.0513395
X-RAY DIFFRACTIONr_scbond_it2.7122.9072500
X-RAY DIFFRACTIONr_scbond_other2.7122.9072501
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9814.2683751
X-RAY DIFFRACTIONr_long_range_B_refined5.36532.3625763
X-RAY DIFFRACTIONr_long_range_B_other5.33432.2265708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10390 / 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: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 157 -
Rwork0.259 3153 -
obs--99.94 %

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