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- PDB-7zbo: Amine Dehydrogenase MATOUAmDH2 in complex with NADP+ -

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Basic information

Entry
Database: PDB / ID: 7zbo
TitleAmine Dehydrogenase MATOUAmDH2 in complex with NADP+
ComponentsAmine Dehydrogenase
KeywordsOXIDOREDUCTASE / Amine / NADP+ / dehydrogenase
Function / homologyNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsBennett, M. / Ducrot, L. / Vergne-Vaxelaire, 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
DepositionMar 24, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
C: Amine Dehydrogenase
D: Amine Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,9718
Polymers152,9974
Non-polymers2,9744
Water4,234235
1
A: Amine Dehydrogenase
D: Amine Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9854
Polymers76,4992
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-41 kcal/mol
Surface area27580 Å2
MethodPISA
2
B: Amine Dehydrogenase
C: Amine Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9854
Polymers76,4992
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-42 kcal/mol
Surface area26320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.098, 112.195, 153.146
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROARGARGAA9 - 3509 - 350
21PROPROARGARGBB9 - 3509 - 350
12SERSERLEULEUAA8 - 3518 - 351
22SERSERLEULEUCC8 - 3518 - 351
13SERSERLEULEUAA8 - 3518 - 351
23SERSERLEULEUDD8 - 3518 - 351
14PROPROLEULEUBB9 - 3519 - 351
24PROPROLEULEUCC9 - 3519 - 351
15PROPROLEULEUBB9 - 3519 - 351
25PROPROLEULEUDD9 - 3519 - 351
16SERSERLEULEUCC8 - 3518 - 351
26SERSERLEULEUDD8 - 3518 - 351

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Amine Dehydrogenase


Mass: 38249.332 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: EC: 1.4.9.98
#2: 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium sulfate; 0.1 M bis-tris propane; 25% (w/v) PEG3350; 10% (v/v) methylpentanediol

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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 EIGER2 XE 16M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.32→64.21 Å / Num. obs: 68673 / % possible obs: 100 % / Redundancy: 8.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.14 / Net I/σ(I): 5.8
Reflection shellResolution: 2.32→2.37 Å / Rmerge(I) obs: 1.37 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4580 / CC1/2: 0.68 / Rpim(I) all: 0.74

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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: 2.32→64.21 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.881 / SU B: 11.371 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.384 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2878 3432 5 %RANDOM
Rwork0.2374 ---
obs0.2399 65166 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 178.59 Å2 / Biso mean: 35.175 Å2 / Biso min: 11.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20 Å2
2--4.33 Å2-0 Å2
3----2.83 Å2
Refinement stepCycle: final / Resolution: 2.32→64.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10206 0 192 235 10633
Biso mean--37.58 26.03 -
Num. residues----1371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01310607
X-RAY DIFFRACTIONr_bond_other_d0.0010.0159746
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.65114452
X-RAY DIFFRACTIONr_angle_other_deg1.2881.57422513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.86151365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6824.587436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.329151687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1681528
X-RAY DIFFRACTIONr_chiral_restr0.0720.21486
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212075
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022189
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A100830.09
12B100830.09
21A99410.11
22C99410.11
31A97600.09
32D97600.09
41B96520.12
42C96520.12
51B95140.1
52D95140.1
61C96660.1
62D96660.1
LS refinement shellResolution: 2.32→2.38 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 271 -
Rwork0.352 4746 -
all-5017 -
obs--99.96 %

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