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- PDB-7xe8: Crystal structure of imine reductase from Streptomyces albidoflavus -

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Basic information

Entry
Database: PDB / ID: 7xe8
TitleCrystal structure of imine reductase from Streptomyces albidoflavus
Components6-phosphogluconate dehydrogenase NAD-binding
KeywordsOXIDOREDUCTASE / Streptomyces albidoflavus / NADP / R-imine reductase
Function / homology3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / NADP binding / oxidoreductase activity / NAD(P)-binding domain superfamily / 6-phosphogluconate dehydrogenase NAD-binding
Function and homology information
Biological speciesStreptomyces albidoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsZhang, J. / Chen, R.C. / Gao, S.S.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentgrant 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
DepositionMar 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,2863
Polymers97,2863
Non-polymers00
Water15,925884
1
C: 6-phosphogluconate dehydrogenase NAD-binding
A: 6-phosphogluconate dehydrogenase NAD-binding


Theoretical massNumber of molelcules
Total (without water)64,8572
Polymers64,8572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8240 Å2
ΔGint-73 kcal/mol
Surface area21370 Å2
MethodPISA
2
B: 6-phosphogluconate dehydrogenase NAD-binding

B: 6-phosphogluconate dehydrogenase NAD-binding


Theoretical massNumber of molelcules
Total (without water)64,8572
Polymers64,8572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area7970 Å2
ΔGint-76 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.487, 65.819, 126.874
Angle α, β, γ (deg.)90.000, 103.772, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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.: 3
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 884 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M ammonium acetate, 0.1M Bis Tris pH5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.72→27.07 Å / Num. obs: 90868 / % possible obs: 96.62 % / Redundancy: 6.4 % / Biso Wilson estimate: 25.84 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03601 / Rpim(I) all: 0.01497 / Rrim(I) all: 0.03908 / Net I/σ(I): 28.13
Reflection shellResolution: 1.72→1.781 Å / Rmerge(I) obs: 0.4187 / Mean I/σ(I) obs: 2.75 / Num. unique obs: 8782 / CC1/2: 0.2118

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zgy

3zgy


Resolution: 1.72→27.07 Å / SU ML: 0.1679 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.6516
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2015 1980 2.18 %
Rwork0.1724 88786 -
obs0.1731 90766 95.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.91 Å2
Refinement stepCycle: LAST / Resolution: 1.72→27.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6130 0 0 884 7014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00856238
X-RAY DIFFRACTIONf_angle_d1.01638515
X-RAY DIFFRACTIONf_chiral_restr0.06441006
X-RAY DIFFRACTIONf_plane_restr0.01041130
X-RAY DIFFRACTIONf_dihedral_angle_d5.2325923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.760.2791190.22775903X-RAY DIFFRACTION89.43
1.76-1.810.24971460.2086171X-RAY DIFFRACTION93.82
1.81-1.860.25731420.2066183X-RAY DIFFRACTION94.53
1.86-1.920.2221460.20146297X-RAY DIFFRACTION95.61
1.92-1.990.26221350.19796327X-RAY DIFFRACTION95.78
1.99-2.070.23821450.18966327X-RAY DIFFRACTION96.17
2.07-2.160.24151400.19016337X-RAY DIFFRACTION96.43
2.16-2.280.22021380.18036351X-RAY DIFFRACTION96.59
2.28-2.420.21361450.17996399X-RAY DIFFRACTION96.99
2.42-2.610.20611540.18486412X-RAY DIFFRACTION97.4
2.61-2.870.23111430.18816469X-RAY DIFFRACTION97.58
2.87-3.280.19741380.17816499X-RAY DIFFRACTION97.91
3.28-4.130.16021450.15036529X-RAY DIFFRACTION97.96
4.13-27.070.17351440.14696582X-RAY DIFFRACTION96.97

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