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- PDB-5ocm: Imine Reductase from Streptosporangium roseum in complex with NAD... -

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Basic information

Entry
Database: PDB / ID: 5ocm
TitleImine Reductase from Streptosporangium roseum in complex with NADP+ and 2,2,2-trifluoroacetophenone hydrate
ComponentsNAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Imine / Amine / NADPH
Function / homology
Function and homology information


NADP binding / oxidoreductase activity
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
2,2,2-trifluoromethyl acetophenone hydrate / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptosporangium roseum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsSharma, M. / Nestl, B. / Grogan, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M006832/1 United Kingdom
CitationJournal: Protein Eng. Des. Sel. / Year: 2018
Title: New imine-reducing enzymes from beta-hydroxyacid dehydrogenases by single amino acid substitutions.
Authors: Lenz, M. / Fademrecht, S. / Sharma, M. / Pleiss, J. / Grogan, G. / Nestl, B.M.
History
DepositionJul 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _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: NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase
B: NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase
C: NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase
D: NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase
E: NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase
F: NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,02725
Polymers180,2446
Non-polymers5,78319
Water20,5191139
1
A: NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase
F: NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0018
Polymers60,0812
Non-polymers1,9206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-95 kcal/mol
Surface area19830 Å2
MethodPISA
2
B: NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase
C: NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9777
Polymers60,0812
Non-polymers1,8955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12130 Å2
ΔGint-100 kcal/mol
Surface area19930 Å2
MethodPISA
3
D: NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase
E: NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,05010
Polymers60,0812
Non-polymers1,9688
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12080 Å2
ΔGint-109 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.811, 152.434, 251.598
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

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
11ARGARGPROPROAA2 - 2892 - 289
21ARGARGPROPROBB2 - 2892 - 289
12ARGARGSERSERAA2 - 2882 - 288
22ARGARGSERSERCC2 - 2882 - 288
13ARGARGPROPROAA2 - 2892 - 289
23ARGARGPROPRODD2 - 2892 - 289
14ARGARGPHEPHEAA2 - 2862 - 286
24ARGARGPHEPHEEE2 - 2862 - 286
15ASPASPPROPROAA3 - 2893 - 289
25ASPASPPROPROFF3 - 2893 - 289
16ARGARGSERSERBB2 - 2882 - 288
26ARGARGSERSERCC2 - 2882 - 288
17METMETSERSERBB1 - 2901 - 290
27METMETSERSERDD1 - 2901 - 290
18ARGARGPHEPHEBB2 - 2862 - 286
28ARGARGPHEPHEEE2 - 2862 - 286
19ASPASPPROPROBB3 - 2893 - 289
29ASPASPPROPROFF3 - 2893 - 289
110ARGARGSERSERCC2 - 2882 - 288
210ARGARGSERSERDD2 - 2882 - 288
111ARGARGPHEPHECC2 - 2862 - 286
211ARGARGPHEPHEEE2 - 2862 - 286
112ASPASPSERSERCC3 - 2883 - 288
212ASPASPSERSERFF3 - 2883 - 288
113ARGARGPHEPHEDD2 - 2862 - 286
213ARGARGPHEPHEEE2 - 2862 - 286
114ASPASPPROPRODD3 - 2893 - 289
214ASPASPPROPROFF3 - 2893 - 289
115ASPASPPHEPHEEE3 - 2863 - 286
215ASPASPPHEPHEFF3 - 2863 - 286

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase / Imine Reductase


Mass: 30040.674 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptosporangium roseum (bacteria) / Gene: Sros_0924 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D2B7Z8
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-9RH / 2,2,2-trifluoromethyl acetophenone hydrate


Mass: 192.135 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H7F3O2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1139 / 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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris-HCl pH 8.0; 20% PEG 6000; 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.81→125.8 Å / Num. obs: 161732 / % possible obs: 100 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.06 / Net I/σ(I): 13.7
Reflection shellResolution: 1.81→1.84 Å / Rmerge(I) obs: 0.85 / Num. unique obs: 7938 / Rpim(I) all: 0.48

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZHB

3zhb


Resolution: 1.81→125.8 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.528 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.109 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19573 8058 5 %RANDOM
Rwork0.16812 ---
obs0.16947 153606 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.477 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0 Å20 Å2
2---0.88 Å2-0 Å2
3---1.51 Å2
Refinement stepCycle: 1 / Resolution: 1.81→125.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12443 0 373 1139 13955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01913074
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211844
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.97717941
X-RAY DIFFRACTIONr_angle_other_deg1.082.99727209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.90351730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1523.937475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.845151769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4211566
X-RAY DIFFRACTIONr_chiral_restr0.1470.22118
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022684
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_it1.8121.8236926
X-RAY DIFFRACTIONr_mcbond_other1.8111.8236925
X-RAY DIFFRACTIONr_mcangle_it2.4112.7228648
X-RAY DIFFRACTIONr_mcangle_other2.4112.7228649
X-RAY DIFFRACTIONr_scbond_it2.8712.0896148
X-RAY DIFFRACTIONr_scbond_other2.8712.0896146
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1673.0219289
X-RAY DIFFRACTIONr_long_range_B_refined4.82522.78715019
X-RAY DIFFRACTIONr_long_range_B_other4.82522.78615020
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A170080.07
12B170080.07
21A172540.06
22C172540.06
31A170000.07
32D170000.07
41A170440.07
42E170440.07
51A168780.07
52F168780.07
61B168820.08
62C168820.08
71B170440.07
72D170440.07
81B169420.07
82E169420.07
91B169880.06
92F169880.06
101C170000.06
102D170000.06
111C170620.06
112E170620.06
121C168120.07
122F168120.07
131D169200.06
132E169200.06
141D169900.06
142F169900.06
151E167660.07
152F167660.07
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 601 -
Rwork0.254 11308 -
obs--100 %

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