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- PDB-7qzn: Amine Dehydrogenase from Cystobacter fuscus (CfusAmDH) W145A muta... -

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Basic information

Entry
Database: PDB / ID: 7qzn
TitleAmine Dehydrogenase from Cystobacter fuscus (CfusAmDH) W145A mutant with NAD+
ComponentsAmine Dehydrogenase
KeywordsOXIDOREDUCTASE / Amine Dehydrogenase / NADP
Function / homology2,4-diaminopentanoate dehydrogenase, C-terminal domain / 2,4-diaminopentanoate dehydrogenase C-terminal domain / NAD(P)-binding domain superfamily / nucleotide binding / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2,4-diaminopentanoate dehydrogenase C-terminal domain-containing protein
Function and homology information
Biological speciesCystobacter fuscus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsBennett, M. / Ducrot, L. / Vaxelaire-Vergne, C. / Grogan, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chemcatchem / Year: 2022
Title: Cover Feature: Expanding the Substrate Scope of Native Amine Dehydrogenases through In Silico Structural Exploration and Targeted Protein Engineering (ChemCatChem 22/2022)
Authors: Ducrot, L. / Bennett, M. / Andre-Leroux, G. / Elisee, E. / Marynberg, S. / Fossey-Jouenne, A. / Zaparucha, A. / Grogan, G. / Vergne-Vaxelaire, C.
History
DepositionJan 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1536
Polymers74,5822
Non-polymers1,5714
Water10,953608
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-28 kcal/mol
Surface area24970 Å2
Unit cell
Length a, b, c (Å)51.017, 86.227, 142.939
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

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / 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: 2 - 342 / Label seq-ID: 6 - 346

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

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Components

#1: Protein Amine Dehydrogenase


Mass: 37291.008 Da / Num. of mol.: 2 / Mutation: W145A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cystobacter fuscus (bacteria) / Gene: D187_009359 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S9Q235
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0. 1 M Tris-HCl pH 8.5; 0.2 M MgCl2; 8% (w/v) PEG 20000; 8% (v/v) PEG 500 MME; 10 mM NAD

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976261 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976261 Å / Relative weight: 1
ReflectionResolution: 1.64→48.09 Å / Num. obs: 78152 / % possible obs: 100 % / Redundancy: 11.8 % / Biso Wilson estimate: 22 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Net I/σ(I): 19.1
Reflection shellResolution: 1.64→1.67 Å / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 2 / Num. unique obs: 3786 / CC1/2: 0.73 / Rpim(I) all: 0.54

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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: 1.64→48.09 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.222 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 3858 5 %RANDOM
Rwork0.1786 ---
obs0.1804 73972 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.49 Å2 / Biso mean: 26.297 Å2 / Biso min: 7.28 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.63 Å2-0 Å2
3----0.64 Å2
Refinement stepCycle: final / Resolution: 1.64→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5102 0 104 612 5818
Biso mean--40.6 37.86 -
Num. residues----682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135323
X-RAY DIFFRACTIONr_bond_other_d0.0010.0144966
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.6497286
X-RAY DIFFRACTIONr_angle_other_deg1.4941.57411368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9065682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78620.824267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29215786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0231547
X-RAY DIFFRACTIONr_chiral_restr0.0910.2741
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026110
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021222
Refine LS restraints NCS

Ens-ID: 1 / Number: 10454 / 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: 1.64→1.683 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 249 -
Rwork0.248 5405 -
all-5654 -
obs--99.98 %

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