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- PDB-8qhe: Crystal structure IR-09 -

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Basic information

Entry
Database: PDB / ID: 8qhe
TitleCrystal structure IR-09
Components6-phosphogluconate dehydrogenase NADP-binding domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / 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-NDP / ~{N}-methylcyclohexanamine / 6-phosphogluconate dehydrogenase NADP-binding domain-containing protein
Similarity search - Component
Biological speciesAspergillus lentulus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLevy, C.W.
Funding supportEuropean Union, United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council (ERC)742987European Union
Biotechnology and Biological Sciences Research Council (BBSRC)EP/S005226/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Biocatalysis in Drug Design: Engineered Reductive Aminases (RedAms) Are Used to Access Chiral Building Blocks with Multiple Stereocenters.
Authors: Casamajo, A.R. / Yu, Y. / Schnepel, C. / Morrill, C. / Barker, R. / Levy, C.W. / Finnigan, J. / Spelling, V. / Westerlund, K. / Petchey, M. / Sheppard, R.J. / Lewis, R.J. / Falcioni, F. / ...Authors: Casamajo, A.R. / Yu, Y. / Schnepel, C. / Morrill, C. / Barker, R. / Levy, C.W. / Finnigan, J. / Spelling, V. / Westerlund, K. / Petchey, M. / Sheppard, R.J. / Lewis, R.J. / Falcioni, F. / Hayes, M.A. / Turner, N.J.
History
DepositionSep 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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 NADP-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0694
Polymers32,1861
Non-polymers8833
Water2,864159
1
A: 6-phosphogluconate dehydrogenase NADP-binding domain-containing protein
hetero molecules

A: 6-phosphogluconate dehydrogenase NADP-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1378
Polymers64,3712
Non-polymers1,7666
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area11380 Å2
ΔGint-108 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.255, 101.104, 36.388
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein 6-phosphogluconate dehydrogenase NADP-binding domain-containing protein


Mass: 32185.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus lentulus (mold) / Gene: ALT_005006 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S7DXU4
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-VCU / ~{N}-methylcyclohexanamine


Mass: 113.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15N
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate 0.1 M Tris 8.5 20 % w/v PEG 8000
Temp details: Cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.6→36.89 Å / Num. obs: 39488 / % possible obs: 99.81 % / Redundancy: 12.4 % / Biso Wilson estimate: 31.34 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.025 / Net I/σ(I): 12.24
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 11.9 % / Mean I/σ(I) obs: 1.16 / Num. unique obs: 3920 / CC1/2: 0.536 / Rpim(I) all: 0.702 / % possible all: 99.16

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→36.89 Å / SU ML: 0.2017 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9478
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2113 2019 5.12 %
Rwork0.182 37416 -
obs0.1834 39435 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.35 Å2
Refinement stepCycle: LAST / Resolution: 1.6→36.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 0 57 159 2312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01962236
X-RAY DIFFRACTIONf_angle_d1.69193046
X-RAY DIFFRACTIONf_chiral_restr0.0934358
X-RAY DIFFRACTIONf_plane_restr0.0116383
X-RAY DIFFRACTIONf_dihedral_angle_d15.5496327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.33321350.30742590X-RAY DIFFRACTION97.81
1.64-1.680.28081420.27532624X-RAY DIFFRACTION99.5
1.68-1.730.29621520.25232654X-RAY DIFFRACTION99.79
1.73-1.790.31141450.24552589X-RAY DIFFRACTION99.64
1.79-1.850.30171610.25422626X-RAY DIFFRACTION99.75
1.85-1.930.28531410.25822640X-RAY DIFFRACTION99.89
1.93-2.010.29051440.21652656X-RAY DIFFRACTION99.96
2.02-2.120.22261330.20232662X-RAY DIFFRACTION99.89
2.12-2.250.21051470.19912669X-RAY DIFFRACTION100
2.25-2.430.26611310.19792698X-RAY DIFFRACTION99.93
2.43-2.670.20971460.17972667X-RAY DIFFRACTION100
2.67-3.060.21181440.19272725X-RAY DIFFRACTION100
3.06-3.850.21671430.16592725X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.332274380715-0.04703829740760.1006562816510.1521663208240.05078436640710.1724761405530.175130869666-0.2153191551180.03476056704580.4267178036390.147122055684-0.104842450951-0.1025551947350.4615874969240.0003812736854690.404846051120.0047270471864-0.009468073339660.356446715813-0.07902301245250.32656556835293.0933452367-28.059754309549.9243544235
20.520589380244-0.4771477213310.1842226545610.556608690451-0.1674868364480.1742434569950.174970597138-0.09993690111390.1286267608720.2936155317730.18599355957-0.124627052430.1050321331430.5576873111480.0006343157937340.3822520898180.0450462877407-0.08122480537220.449917305184-0.1198797968240.31933058986999.45025634-29.525456366746.4780849344
32.45263400481-0.8704108710380.07528071035881.94242294099-0.1793448513182.517372243250.200908598107-0.0156180495196-0.4557335884880.1613510908170.06639336248710.4635329821790.176792293501-0.05539901620890.0175348871510.307100615294-0.03669242773160.01333002385350.234647917347-0.03087949208220.41873722885883.007468757-29.534279572842.9406297383
40.505809761545-0.3031908655910.3406924381080.269528922432-0.0398147677280.505774365148-0.126084108223-0.08584428287360.0452327650579-0.145863175307-0.2007410153940.05408811843380.01087297160270.203982597737-0.001634947500760.275974817962-0.00695266492930.02513467130110.2616373685710.02177977846280.27490221841884.1502036078-1.3927711399339.2217377798
52.032777977220.6071938989390.5869513565893.336666511410.2640968312871.91580615080.0408579915424-0.2956489272920.3754012430780.368310601755-0.6967745645250.551102887866-0.3381667987-0.550554596739-1.85565046950.241397313949-0.101615714182-0.0160664847030.654379365623-0.1567128829190.24647987297675.08365015143.9205674769446.9233458251
60.149375986043-0.206344063107-0.081360699141.117885038980.6799350177550.4231977041330.429098031446-0.254489065776-0.3139048632870.117045991352-0.4652327232130.463096169826-0.195086161763-0.2446673222910.005355178836770.311238535432-0.0165740930288-0.07482163328360.3393385440070.02161946895790.37895929152871.363411231411.511355704734.4519168185
70.1078790131160.3400839740210.162798716761.13115763110.2036225547090.955436322028-0.210396556002-0.1176171476210.567795392644-0.58859191005-0.08889772516530.599162300612-0.246423315338-0.358472792767-0.08774236830530.3954376668570.0411327091075-0.1363823958350.369038337595-0.05628458745610.37862997562369.88741590273.7330083116730.227338456
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 22 )1 - 221 - 22
22chain 'A' and (resid 23 through 43 )23 - 4323 - 43
33chain 'A' and (resid 44 through 161 )44 - 16144 - 161
44chain 'A' and (resid 162 through 193 )162 - 193162 - 193
55chain 'A' and (resid 194 through 221 )194 - 221194 - 221
66chain 'A' and (resid 222 through 248 )222 - 248222 - 248
77chain 'A' and (resid 249 through 284 )249 - 284249 - 284

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