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- PDB-7xr5: Crystal structure of imine reductase with NAPDH from Streptomyces... -

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Basic information

Entry
Database: PDB / ID: 7xr5
TitleCrystal structure of imine reductase with NAPDH from Streptomyces albidoflavus
Components6-phosphogluconate dehydrogenase NAD-binding
KeywordsOXIDOREDUCTASE / Streptomyces albidoflavus / NADP / R-imine reductase
Function / homology
Function and homology information


NADP binding / oxidoreductase activity
Similarity search - Function
3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-9FO / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 6-phosphogluconate dehydrogenase NAD-binding
Similarity search - Component
Biological speciesStreptomyces albidoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsZhang, J. / Chen, R.C. / Gao, S.S.
Funding support China, 1items
OrganizationGrant numberCountry
Other government(grant nos. 31872614 and 31600270 China
CitationJournal: Commun Chem / Year: 2022
Title: Actinomycetes-derived imine reductases with a preference towards bulky amine substrates.
Authors: Zhang, J. / Li, X. / Chen, R. / Tan, X. / Liu, X. / Ma, Y. / Zhu, F. / An, C. / Wei, G. / Yao, Y. / Yang, L. / Zhang, P. / Wu, Q. / Sun, Z. / Wang, B.G. / Gao, S.S. / Cui, C.
History
DepositionMay 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-phosphogluconate dehydrogenase NAD-binding
B: 6-phosphogluconate dehydrogenase NAD-binding
C: 6-phosphogluconate dehydrogenase NAD-binding
D: 6-phosphogluconate dehydrogenase NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,48610
Polymers129,7144
Non-polymers4,7726
Water20,2131122
1
A: 6-phosphogluconate dehydrogenase NAD-binding
B: 6-phosphogluconate dehydrogenase NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2435
Polymers64,8572
Non-polymers2,3863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10370 Å2
ΔGint-76 kcal/mol
Surface area22380 Å2
MethodPISA
2
C: 6-phosphogluconate dehydrogenase NAD-binding
D: 6-phosphogluconate dehydrogenase NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2435
Polymers64,8572
Non-polymers2,3863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10190 Å2
ΔGint-70 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.282, 120.013, 76.458
Angle α, β, γ (deg.)90.000, 117.178, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein
6-phosphogluconate dehydrogenase NAD-binding / 6-phosphogluconate dehydrogenase NAD-binding protein


Mass: 32428.541 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albidoflavus (bacteria) / Gene: SSHG_01979, XNRR2_3955 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6B3A0
#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: Chemical ChemComp-9FO / 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57-nonadecaoxanonapentacontane-1,59-diol


Mass: 899.066 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H82O21
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1122 / 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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7.5 / Details: 0.1M Bis-Tris ph7.5, 25% PEG 4000 0.25M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.58→34.46 Å / Num. obs: 166817 / % possible obs: 98.64 % / Redundancy: 5.1 % / Biso Wilson estimate: 18.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.62
Reflection shellResolution: 1.58→1.636 Å / Rmerge(I) obs: 0.8942 / Mean I/σ(I) obs: 2.59 / Num. unique obs: 16450 / CC1/2: 0.662

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XE8

7xe8


Resolution: 1.58→34.46 Å / SU ML: 0.1722 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9093
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2015 8111 4.88 %
Rwork0.1791 158076 -
obs0.1802 166187 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.34 Å2
Refinement stepCycle: LAST / Resolution: 1.58→34.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8173 0 302 1122 9597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00678640
X-RAY DIFFRACTIONf_angle_d1.090811793
X-RAY DIFFRACTIONf_chiral_restr0.05421377
X-RAY DIFFRACTIONf_plane_restr0.0091521
X-RAY DIFFRACTIONf_dihedral_angle_d7.17571330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.590.29312530.25225298X-RAY DIFFRACTION97.78
1.59-1.610.29012700.24755175X-RAY DIFFRACTION98.86
1.61-1.630.27682820.23565338X-RAY DIFFRACTION98.93
1.63-1.650.24252560.22125272X-RAY DIFFRACTION99.03
1.65-1.670.22862760.21665289X-RAY DIFFRACTION99.29
1.67-1.70.2522890.21655285X-RAY DIFFRACTION99.34
1.7-1.720.26342670.22415252X-RAY DIFFRACTION99.32
1.72-1.750.26562600.23075284X-RAY DIFFRACTION99
1.75-1.770.27222590.22115348X-RAY DIFFRACTION99.01
1.77-1.80.25882130.21475281X-RAY DIFFRACTION99.03
1.8-1.830.24642570.20845277X-RAY DIFFRACTION98.68
1.83-1.870.26032080.20525262X-RAY DIFFRACTION97
1.87-1.90.25092380.2085244X-RAY DIFFRACTION98.12
1.9-1.940.22162760.19975287X-RAY DIFFRACTION99.25
1.94-1.980.2092680.19415235X-RAY DIFFRACTION99.15
1.98-2.030.20212730.18925329X-RAY DIFFRACTION99.13
2.03-2.080.22233060.19095253X-RAY DIFFRACTION99.32
2.08-2.140.21882640.18115343X-RAY DIFFRACTION99.54
2.14-2.20.20322520.17445280X-RAY DIFFRACTION99.23
2.2-2.270.19442680.17855293X-RAY DIFFRACTION98.69
2.27-2.350.21412850.17985207X-RAY DIFFRACTION97.93
2.35-2.450.21032700.18015178X-RAY DIFFRACTION97.2
2.45-2.560.22332560.18295362X-RAY DIFFRACTION99.14
2.56-2.690.21472800.18425226X-RAY DIFFRACTION98.94
2.69-2.860.21262840.17845289X-RAY DIFFRACTION98.95
2.86-3.080.20333470.18255240X-RAY DIFFRACTION99.06
3.08-3.390.18153220.1755109X-RAY DIFFRACTION96.72
3.39-3.880.16112890.15135219X-RAY DIFFRACTION97.18
3.88-4.890.14872780.13995313X-RAY DIFFRACTION98.89
4.89-34.460.17392650.15715308X-RAY DIFFRACTION97.18

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