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- PDB-6h7p: Reductive Aminase from Aspergillus terreus in complex with NADPH4... -

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Basic information

Entry
Database: PDB / ID: 6h7p
TitleReductive Aminase from Aspergillus terreus in complex with NADPH4, cyclohexanone and allyl amine
ComponentsReductive Aminase
KeywordsOXIDOREDUCTASE / Amine / Imine / NADPH
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NADP binding
Similarity search - Function
: / NADPH-dependent reductive aminase-like, C-terminal domain / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding Rossmann-like Domain ...: / NADPH-dependent reductive aminase-like, C-terminal domain / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
prop-2-en-1-amine / CYCLOHEXANONE / Chem-FVH / Uncharacterized protein
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsSharma, M. / Grogan, G. / Mangas-Sanchez, J. / Turner, N.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
BB/M006611/1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2018
Title: Structure of Reductive Aminase from Aspergillus terreus
Authors: Sharma, M. / Mangas-Sanchez, J. / Turner, N.J. / Grogan, G.
History
DepositionJul 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 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

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Assembly

Deposited unit
A: Reductive Aminase
B: Reductive Aminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2237
Polymers61,5122
Non-polymers1,7115
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-84 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.206, 162.830, 49.681
Angle α, β, γ (deg.)90.00, 108.67, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 6 - 294 / Label seq-ID: 6 - 294

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

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Components

#1: Protein Reductive Aminase


Mass: 30756.084 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Gene: ATEG_08501 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0CCT3
#2: Chemical ChemComp-FVH / [[(2~{R},3~{S},4~{R},5~{R})-5-[(3~{R})-3-aminocarbonylpiperidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate


Mass: 749.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H34N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7N / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CYH / CYCLOHEXANONE


Mass: 98.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM Tris-HCl pH 8.5, 34% PEG 3350, 0.2M MgCl2

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.79→47.07 Å / Num. obs: 52888 / % possible obs: 95.8 % / Redundancy: 3.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.05 / Net I/σ(I): 10.5
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3236 / CC1/2: 0.94 / Rpim(I) all: 0.27 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EOD

6eod


Resolution: 1.79→40.74 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.897 / SU B: 5.862 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.154 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27175 2474 4.9 %RANDOM
Rwork0.24734 ---
obs0.24858 47890 91.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.496 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å2-1.82 Å2
2---2.74 Å20 Å2
3---3.38 Å2
Refinement stepCycle: 1 / Resolution: 1.79→40.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4057 0 111 169 4337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0144244
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173894
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.6495788
X-RAY DIFFRACTIONr_angle_other_deg0.9461.6339036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3465559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83821.772158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3815617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4831520
X-RAY DIFFRACTIONr_chiral_restr0.0730.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024767
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02763
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_it1.9952.8042254
X-RAY DIFFRACTIONr_mcbond_other1.9942.8032253
X-RAY DIFFRACTIONr_mcangle_it3.0044.1892807
X-RAY DIFFRACTIONr_mcangle_other3.0044.1912808
X-RAY DIFFRACTIONr_scbond_it2.5693.1061990
X-RAY DIFFRACTIONr_scbond_other2.5693.1061991
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9244.5422982
X-RAY DIFFRACTIONr_long_range_B_refined5.51633.9774576
X-RAY DIFFRACTIONr_long_range_B_other5.49133.934556
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8293 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 179 -
Rwork0.299 3876 -
obs--99.83 %

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