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- PDB-7r09: Amine Dehydrogenase MATOUAmDH2 in complex with NADP+ and Cyclohex... -

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Basic information

Entry
Database: PDB / ID: 7r09
TitleAmine Dehydrogenase MATOUAmDH2 in complex with NADP+ and Cyclohexylamine
ComponentsAmine Dehydrogenase
KeywordsOXIDOREDUCTASE / Amine / NADP
Function / homologyCYCLOHEXYLAMMONIUM ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsBennett, M. / Ducrot, L. / Vaxelaire-Vergne, C. / Grogan, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chembiochem / Year: 2022
Title: Structure and Mutation of the Native Amine Dehydrogenase MATOUAmDH2.
Authors: Bennett, M. / Ducrot, L. / Vergne-Vaxelaire, C. / Grogan, G.
History
DepositionFeb 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 1, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amine Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0933
Polymers38,2491
Non-polymers8442
Water1,45981
1
A: Amine Dehydrogenase
hetero molecules

A: Amine Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1866
Polymers76,4992
Non-polymers1,6874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area6810 Å2
ΔGint-28 kcal/mol
Surface area25850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.508, 93.508, 75.786
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Amine Dehydrogenase


Mass: 38249.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: EC: 1.4.99.3
#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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M bis-Tris pH 6.5, 25% (w/v) PEG 3350 0.2 M MgCl2, 10 mM NADP, 10 mM n-pentylamine

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.08→55.4 Å / Num. obs: 23365 / % possible obs: 99.9 % / Redundancy: 20.2 % / Biso Wilson estimate: 48 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.02 / Net I/σ(I): 24.4
Reflection shellResolution: 2.08→2.13 Å / Redundancy: 20.7 % / Rmerge(I) obs: 1.28 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1768 / CC1/2: 0.94 / Rpim(I) all: 0.41

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IAU

6iau


Resolution: 2.08→55.4 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.784 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2977 1089 4.7 %RANDOM
Rwork0.2325 ---
obs0.2354 22275 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.88 Å2 / Biso mean: 54.816 Å2 / Biso min: 28.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20.95 Å2-0 Å2
2--1.9 Å20 Å2
3----6.16 Å2
Refinement stepCycle: final / Resolution: 2.08→55.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2563 0 55 83 2701
Biso mean--50.9 57.16 -
Num. residues----344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132670
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152469
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.6513641
X-RAY DIFFRACTIONr_angle_other_deg1.2441.5735695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9045343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18124.273110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47715419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.359158
X-RAY DIFFRACTIONr_chiral_restr0.0540.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023035
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02556
LS refinement shellResolution: 2.08→2.134 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 90 -
Rwork0.374 1600 -
all-1690 -
obs--99.94 %

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