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- PDB-8ix9: Pseudomoans Aerugiona Wildtype Ketopantoate Reductase with NADPH -

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Basic information

Entry
Database: PDB / ID: 8ix9
TitlePseudomoans Aerugiona Wildtype Ketopantoate Reductase with NADPH
Components2-dehydropantoate 2-reductase
KeywordsOXIDOREDUCTASE / PanE2 / PaKPRWT / Ketopantoate Reductase / Pantothenate pathway enzyme.
Function / homologyFORMIC ACID / Chem-NDP / :
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.198 Å
AuthorsChoudhury, G.B. / Datta, S.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: Biochemistry / Year: 2024
Title: Implication of Molecular Constraints Facilitating the Functional Evolution of Pseudomonas aeruginosa KPR2 into a Versatile alpha-Keto-Acid Reductase.
Authors: Basu Choudhury, G. / Datta, S.
History
DepositionMar 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 31, 2024Group: 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
B: 2-dehydropantoate 2-reductase
A: 2-dehydropantoate 2-reductase
C: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,45016
Polymers102,6163
Non-polymers2,83513
Water13,097727
1
B: 2-dehydropantoate 2-reductase
hetero molecules

B: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,45412
Polymers68,4102
Non-polymers2,04310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1820 Å2
ΔGint-8 kcal/mol
Surface area24970 Å2
MethodPISA
2
A: 2-dehydropantoate 2-reductase
hetero molecules

C: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,22310
Polymers68,4102
Non-polymers1,8138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555x+1/2,y+1/2,z1
Buried area1910 Å2
ΔGint-9 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.226, 48.153, 128.305
Angle α, β, γ (deg.)90.00, 129.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 2-dehydropantoate 2-reductase


Mass: 34205.191 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: K3T18_18035 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A8G2Q7Q1
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 727 / 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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 200mM Ammonium Formate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Sep 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.198→26.12 Å / Num. obs: 90500 / % possible obs: 98.8 % / Redundancy: 8.2 % / CC1/2: 0.995 / Net I/σ(I): 11.3
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 4378 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
PROTEUMdata reduction
PROTEUMdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.198→25.109 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2101 3894 4.37 %
Rwork0.1763 --
obs0.1778 89046 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.198→25.109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7117 0 183 727 8027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047470
X-RAY DIFFRACTIONf_angle_d0.67610148
X-RAY DIFFRACTIONf_dihedral_angle_d6.7414393
X-RAY DIFFRACTIONf_chiral_restr0.041093
X-RAY DIFFRACTIONf_plane_restr0.0041325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1981-2.22490.29751360.24842686X-RAY DIFFRACTION90
2.2249-2.2530.2751250.23273041X-RAY DIFFRACTION98
2.253-2.28270.24971680.2183039X-RAY DIFFRACTION98
2.2827-2.31390.23571080.21913014X-RAY DIFFRACTION99
2.3139-2.34690.2251470.22032984X-RAY DIFFRACTION98
2.3469-2.38190.28981460.21263045X-RAY DIFFRACTION99
2.3819-2.41910.26571380.21373086X-RAY DIFFRACTION99
2.4191-2.45880.2631370.2122994X-RAY DIFFRACTION99
2.4588-2.50110.27081430.21073075X-RAY DIFFRACTION99
2.5011-2.54660.24521470.22063072X-RAY DIFFRACTION99
2.5466-2.59550.24961250.20782995X-RAY DIFFRACTION99
2.5955-2.64840.25791390.20413018X-RAY DIFFRACTION99
2.6484-2.70590.22221460.20113072X-RAY DIFFRACTION99
2.7059-2.76880.21591320.19963058X-RAY DIFFRACTION99
2.7688-2.83790.24621510.20493099X-RAY DIFFRACTION99
2.8379-2.91460.23451290.19753047X-RAY DIFFRACTION99
2.9146-3.00020.20711580.18593094X-RAY DIFFRACTION100
3.0002-3.09690.20291320.17393018X-RAY DIFFRACTION100
3.0969-3.20730.22651420.1773105X-RAY DIFFRACTION100
3.2073-3.33550.20861410.16663030X-RAY DIFFRACTION100
3.3355-3.48690.19181300.16313045X-RAY DIFFRACTION100
3.4869-3.67020.2081420.15063107X-RAY DIFFRACTION100
3.6702-3.89940.15631350.13653052X-RAY DIFFRACTION100
3.8994-4.19920.19961330.13633064X-RAY DIFFRACTION100
4.1992-4.61940.14471520.12333082X-RAY DIFFRACTION100
4.6194-5.28240.15151370.13413077X-RAY DIFFRACTION100
5.2824-6.63490.18031440.17823073X-RAY DIFFRACTION100
6.6349-25.10.14971310.13883080X-RAY DIFFRACTION99
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)
11.41-0.55090.66411.6224-0.76661.59180.05470.0729-0.1117-0.053-0.00280.0280.1491-0.0264-0.0330.0869-0.00440.00780.0870.00160.0728-32.69851.48250.2979
23.531-0.2937-0.04370.21940.08110.4736-0.0211-0.21930.24840.06580.0584-0.0625-0.0130.0967-0.0210.11590.003-0.00130.1105-0.00050.1248-15.847911.90524.3611
31.8556-0.29271.47012.664-0.64922.18470.07610.0424-0.1923-0.2097-0.00130.06990.2047-0.0602-0.0880.12430.00360.01160.08480.00370.0993-29.650718.881130.2421
42.4034-0.21730.40110.24030.11530.4506-0.0478-0.10770.03950.01960.059-0.0006-0.0373-0.03020.00040.11760.01560.01120.08730.03020.0851-14.737431.501536.6413
51.662-0.23840.97151.71260.82151.89650.04630.0963-0.18830.07090.0469-0.0570.2540.1427-0.04820.12560.00270.00540.0894-0.02580.1039-56.0281-5.127334.6926
61.7668-0.06050.34661.6311.14092.8034-0.06430.04150.2285-0.1330.0644-0.0264-0.17910.1858-0.02240.10440.00870.00060.0877-0.01920.1157-58.41747.13733.2036
72.4892-0.42670.41321.44160.53152.36080.01150.38550.1409-0.16290.0166-0.0336-0.14040.0346-0.0260.08730.00180.02610.1536-0.00110.1009-78.35067.842328.6263
82.41130.08020.80963.30630.47652.29180.0377-0.22710.18860.21350.0750.1657-0.08560.1565-0.05730.07160.00040.04230.1376-0.05930.1182-84.09979.174440.9269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 5 through 161 )
2X-RAY DIFFRACTION2chain 'B' and (resid 162 through 314 )
3X-RAY DIFFRACTION3chain 'A' and (resid 5 through 96 )
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 314 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 111 )
6X-RAY DIFFRACTION6chain 'C' and (resid 112 through 188 )
7X-RAY DIFFRACTION7chain 'C' and (resid 189 through 283 )
8X-RAY DIFFRACTION8chain 'C' and (resid 284 through 314 )

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