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- PDB-7osn: IRED361 from Micromonospora sp. in complex with NADP+ -

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Basic information

Entry
Database: PDB / ID: 7osn
TitleIRED361 from Micromonospora sp. in complex with NADP+
Components6-phosphogluconate dehydrogenase
KeywordsOXIDOREDUCTASE / amine / NADP / imine
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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 6-phosphogluconate dehydrogenase
Function and homology information
Biological speciesMicromonospora sp. Rc5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsGilio, A.K. / Harawa, V. / Turner, N. / Grogan, G.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Synthesis of Stereoenriched Piperidines via Chemo-Enzymatic Dearomatization of Activated Pyridines.
Authors: Harawa, V. / Thorpe, T.W. / Marshall, J.R. / Sangster, J.J. / Gilio, A.K. / Pirvu, L. / Heath, R.S. / Angelastro, A. / Finnigan, J.D. / Charnock, S.J. / Nafie, J.W. / Grogan, G. / Whitehead, R.C. / Turner, N.J.
History
DepositionJun 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-phosphogluconate dehydrogenase
B: 6-phosphogluconate dehydrogenase
C: 6-phosphogluconate dehydrogenase
D: 6-phosphogluconate dehydrogenase
E: 6-phosphogluconate dehydrogenase
F: 6-phosphogluconate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,84912
Polymers189,3886
Non-polymers4,4606
Water2,954164
1
A: 6-phosphogluconate dehydrogenase
B: 6-phosphogluconate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6164
Polymers63,1292
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-103 kcal/mol
Surface area20150 Å2
MethodPISA
2
C: 6-phosphogluconate dehydrogenase
D: 6-phosphogluconate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6164
Polymers63,1292
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11670 Å2
ΔGint-100 kcal/mol
Surface area20080 Å2
MethodPISA
3
E: 6-phosphogluconate dehydrogenase
F: 6-phosphogluconate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6164
Polymers63,1292
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10660 Å2
ΔGint-91 kcal/mol
Surface area20890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.000, 142.000, 266.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
6-phosphogluconate dehydrogenase


Mass: 31564.719 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora sp. Rc5 (bacteria) / Gene: BSA16_00815 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S8Y2S4
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 20 % PEG 3350 w/v, 0.1 M MgCl2 and 2 mM NADP+

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.55→50.28 Å / Num. obs: 63163 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 55 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.04 / Net I/σ(I): 10.2
Reflection shellResolution: 2.55→2.61 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4397 / CC1/2: 0.97 / Rpim(I) all: 0.26 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OCM

5ocm


Resolution: 2.55→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.307 --
Rwork0.26 --
obs-63163 100 %
Displacement parametersBiso max: 168.7 Å2 / Biso min: 12.9 Å2
Refinement stepCycle: LAST / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12511 0 288 170 12969
LS refinement shellResolution: 2.55→2.61 Å /
RfactorNum. reflection
Rfree0.26 -
Rwork0.307 -
obs-4397

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