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- PDB-6sle: Structure of Reductive Aminase from Neosartorya fumigata in compl... -

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Basic information

Entry
Database: PDB / ID: 6sle
TitleStructure of Reductive Aminase from Neosartorya fumigata in complex with NADP+
ComponentsOxidoreductase, putative
KeywordsOXIDOREDUCTASE / Amine / Imine / NADPH
Function / homology
Function and homology information


3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase activity / transcription elongation-coupled chromatin remodeling / nucleosome binding / NADP binding / chromatin / DNA 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Oxidoreductase, putative
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsSharma, M. / Mangas-Sanchez, J. / Turner, N.J. / Grogan, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M006832/1 United Kingdom
CitationJournal: Chem Sci / Year: 2020
Title: Asymmetric synthesis of primary amines catalyzed by thermotolerant fungal reductive aminases.
Authors: Mangas-Sanchez, J. / Sharma, M. / Cosgrove, S.C. / Ramsden, J.I. / Marshall, J.R. / Thorpe, T.W. / Palmer, R.B. / Grogan, G. / Turner, N.J.
History
DepositionAug 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 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: Oxidoreductase, putative
B: Oxidoreductase, putative
C: Oxidoreductase, putative
D: Oxidoreductase, putative
E: Oxidoreductase, putative
F: Oxidoreductase, putative
G: Oxidoreductase, putative
H: Oxidoreductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,23016
Polymers240,2838
Non-polymers5,9478
Water1,892105
1
A: Oxidoreductase, putative
B: Oxidoreductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5584
Polymers60,0712
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-98 kcal/mol
Surface area21170 Å2
MethodPISA
2
C: Oxidoreductase, putative
H: Oxidoreductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5584
Polymers60,0712
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-102 kcal/mol
Surface area20740 Å2
MethodPISA
3
D: Oxidoreductase, putative
E: Oxidoreductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5584
Polymers60,0712
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9890 Å2
ΔGint-100 kcal/mol
Surface area20530 Å2
MethodPISA
4
F: Oxidoreductase, putative
G: Oxidoreductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5584
Polymers60,0712
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
ΔGint-107 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.387, 89.312, 97.932
Angle α, β, γ (deg.)105.560, 90.000, 93.990
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

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
11SERSERLYSLYSAA3 - 2833 - 283
21SERSERLYSLYSBB3 - 2833 - 283
12METMETLYSLYSAA1 - 2831 - 283
22METMETLYSLYSCC1 - 2831 - 283
13METMETLYSLYSAA1 - 2831 - 283
23METMETLYSLYSDD1 - 2831 - 283
14SERSERLYSLYSAA3 - 2833 - 283
24SERSERLYSLYSEE3 - 2833 - 283
15SERSERVALVALAA2 - 2822 - 282
25SERSERVALVALFF2 - 2822 - 282
16METMETLYSLYSAA1 - 2831 - 283
26METMETLYSLYSGG1 - 2831 - 283
17SERSERLYSLYSAA2 - 2832 - 283
27SERSERLYSLYSHH2 - 2832 - 283
18SERSERLYSLYSBB3 - 2833 - 283
28SERSERLYSLYSCC3 - 2833 - 283
19SERSERLYSLYSBB3 - 2833 - 283
29SERSERLYSLYSDD3 - 2833 - 283
110SERSERLYSLYSBB3 - 2833 - 283
210SERSERLYSLYSEE3 - 2833 - 283
111SERSERLYSLYSBB3 - 2833 - 283
211SERSERLYSLYSFF3 - 2833 - 283
112SERSERLYSLYSBB3 - 2833 - 283
212SERSERLYSLYSGG3 - 2833 - 283
113SERSERLYSLYSBB3 - 2833 - 283
213SERSERLYSLYSHH3 - 2833 - 283
114METMETLYSLYSCC1 - 2831 - 283
214METMETLYSLYSDD1 - 2831 - 283
115SERSERLYSLYSCC3 - 2833 - 283
215SERSERLYSLYSEE3 - 2833 - 283
116SERSERLYSLYSCC2 - 2832 - 283
216SERSERLYSLYSFF2 - 2832 - 283
117METMETLYSLYSCC1 - 2831 - 283
217METMETLYSLYSGG1 - 2831 - 283
118SERSERLYSLYSCC2 - 2832 - 283
218SERSERLYSLYSHH2 - 2832 - 283
119SERSERLYSLYSDD3 - 2833 - 283
219SERSERLYSLYSEE3 - 2833 - 283
120SERSERLYSLYSDD2 - 2832 - 283
220SERSERLYSLYSFF2 - 2832 - 283
121METMETLYSLYSDD1 - 2831 - 283
221METMETLYSLYSGG1 - 2831 - 283
122SERSERLYSLYSDD2 - 2832 - 283
222SERSERLYSLYSHH2 - 2832 - 283
123SERSERLYSLYSEE3 - 2833 - 283
223SERSERLYSLYSFF3 - 2833 - 283
124SERSERLYSLYSEE3 - 2833 - 283
224SERSERLYSLYSGG3 - 2833 - 283
125SERSERLYSLYSEE3 - 2833 - 283
225SERSERLYSLYSHH3 - 2833 - 283
126SERSERLYSLYSFF2 - 2832 - 283
226SERSERLYSLYSGG2 - 2832 - 283
127SERSERLYSLYSFF2 - 2832 - 283
227SERSERLYSLYSHH2 - 2832 - 283
128SERSERLYSLYSGG2 - 2832 - 283
228SERSERLYSLYSHH2 - 2832 - 283

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Oxidoreductase, putative


Mass: 30035.359 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_5G01250 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4WDZ8, 3-hydroxyisobutyrate dehydrogenase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 6000; 0.2 M CaCl2; 0.1M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97631 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97631 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.866
11h,-k,-l20.134
ReflectionResolution: 2.77→48.28 Å / Num. obs: 53924 / % possible obs: 98.1 % / Redundancy: 3.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.14 / Net I/σ(I): 5.2
Reflection shellResolution: 2.77→2.85 Å / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4393 / CC1/2: 0.56 / Rpim(I) all: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E0D

6e0d


Resolution: 2.77→48.28 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.814 / SU B: 16.287 / SU ML: 0.354 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.117
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3573 2664 4.9 %RANDOM
Rwork0.2861 ---
obs0.2896 51230 79.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 163.2 Å2 / Biso mean: 46.425 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--36.06 Å23.91 Å2-3.07 Å2
2--58.05 Å219.32 Å2
3----21.98 Å2
Refinement stepCycle: final / Resolution: 2.77→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14698 0 384 106 15188
Biso mean--40.02 24.92 -
Num. residues----2198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01315351
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713248
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.65720988
X-RAY DIFFRACTIONr_angle_other_deg1.3181.58630266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75852169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54323.297461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.777151860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4721532
X-RAY DIFFRACTIONr_chiral_restr0.0570.22240
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217791
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023101
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A61490.06
12B61490.06
21A69720.05
22C69720.05
31A76010.05
32D76010.05
41A64270.06
42E64270.06
51A76620.04
52F76620.04
61A70420.06
62G70420.06
71A74770.05
72H74770.05
81B60780.06
82C60780.06
91B61450.06
92D61450.06
101B60420.07
102E60420.07
111B60930.06
112F60930.06
121B62040.07
122G62040.07
131B60570.06
132H60570.06
141C69940.05
142D69940.05
151C64920.05
152E64920.05
161C68450.04
162F68450.04
171C67590.05
172G67590.05
181C68930.04
182H68930.04
191D64700.06
192E64700.06
201D74170.04
202F74170.04
211D69340.05
212G69340.05
221D75220.04
222H75220.04
231E63380.06
232F63380.06
241E62900.05
242G62900.05
251E64170.06
252H64170.06
261F69450.05
262G69450.05
271F74290.04
272H74290.04
281G68620.05
282H68620.05
LS refinement shellHighest resolution: 2.77 Å / Rfactor Rfree error: 0

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