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- PDB-8ixh: Pseudomoans aeruginosa Wildtype Ketopantoate Reductase With 3-Met... -

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Basic information

Entry
Database: PDB / ID: 8ixh
TitlePseudomoans aeruginosa Wildtype Ketopantoate Reductase With 3-Methyl-2-oxovalerate at substrate site
Components2-dehydropantoate 2-reductase
KeywordsOXIDOREDUCTASE / PanE2 / 3-Methyl-2-oxovalerate / Ketopantoate Reductase / Pantothenate pathway enzyme
Function / homology(3S)-3-methyl-2-oxopentanoic acid / :
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionApr 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-dehydropantoate 2-reductase
B: 2-dehydropantoate 2-reductase
C: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2829
Polymers102,6163
Non-polymers6676
Water8,305461
1
A: 2-dehydropantoate 2-reductase
hetero molecules

A: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8556
Polymers68,4102
Non-polymers4444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2470 Å2
ΔGint-14 kcal/mol
Surface area24260 Å2
MethodPISA
2
B: 2-dehydropantoate 2-reductase
hetero molecules

C: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8556
Polymers68,4102
Non-polymers4444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1/2,y+1/2,-z1
Buried area2500 Å2
ΔGint-13 kcal/mol
Surface area24200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.206, 47.916, 129.233
Angle α, β, γ (deg.)90.00, 129.68, 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-1QQ / (3S)-3-methyl-2-oxopentanoic acid


Mass: 130.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 44.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 11% PEG 6000, 100mM Hepes ph 7.5, 200mM MgCl2

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.979 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→47.62 Å / Num. obs: 66387 / % possible obs: 99.6 % / Redundancy: 3.8 % / CC1/2: 0.998 / Net I/σ(I): 10.7
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 6616 / CC1/2: 0.632

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
iMOSFLMdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→40.845 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 1695 2.55 %
Rwork0.1971 --
obs0.1977 66369 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→40.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7068 0 45 461 7574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047330
X-RAY DIFFRACTIONf_angle_d0.7769942
X-RAY DIFFRACTIONf_dihedral_angle_d7.4885965
X-RAY DIFFRACTIONf_chiral_restr0.0451070
X-RAY DIFFRACTIONf_plane_restr0.0041325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00740.33981360.29675367X-RAY DIFFRACTION100
2.0074-2.07220.31751430.26385364X-RAY DIFFRACTION100
2.0722-2.14620.28651360.25035354X-RAY DIFFRACTION100
2.1462-2.23220.28581390.22975350X-RAY DIFFRACTION100
2.2322-2.33370.24591490.22065350X-RAY DIFFRACTION100
2.3337-2.45680.25881410.21135380X-RAY DIFFRACTION100
2.4568-2.61070.25051380.21335402X-RAY DIFFRACTION100
2.6107-2.81220.27551450.2115387X-RAY DIFFRACTION100
2.8122-3.09510.24131450.20755367X-RAY DIFFRACTION100
3.0951-3.54270.21271400.18925413X-RAY DIFFRACTION99
3.5427-4.46260.15721420.15835441X-RAY DIFFRACTION99
4.4626-40.8450.18041410.17345499X-RAY DIFFRACTION98
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)
12.20630.55260.95282.10441.12572.79390.097-0.1454-0.10530.1424-0.0033-0.01410.29880.0998-0.09390.22810.02040.01180.2286-0.05960.2068-8.6974-4.025149.4287
25.6079-0.0386-0.36330.0353-0.24110.74370.02160.18830.2138-0.05570.0604-0.00260.0024-0.0069-0.05410.2203-0.01250.02060.2082-0.05120.2596-25.43056.156445.4765
32.56640.6421.09143.63942.21622.98270.1207-0.052-0.350.4667-0.0012-0.08630.49240.0515-0.10940.305-0.00570.00520.2158-0.03240.2111-13.620217.891218.2212
44.64190.51070.68640.7989-0.06260.6573-0.07770.1824-0.1032-0.05490.1217-0.0353-0.02140.0939-0.00880.2098-0.02510.02080.1761-0.04840.149-30.284426.162511.2983
51.7976-1.292.30312.35540.24795.50710.19020.5637-0.3289-0.28370.0383-0.24130.16340.3981-0.21040.22780.0180.03170.2294-0.09750.1985-14.9098-9.3433-19.0718
63.6210.24034.34231.84661.78126.44410.63710.2924-1.00070.46690.1979-0.21741.41010.2622-0.78150.47950.0626-0.04420.3176-0.09110.4283-15.6093-17.2007-19.4739
73.9626-0.85410.39941.83490.72221.8749-0.0158-0.2397-0.12370.27630.0867-0.20150.22570.0662-0.0610.27390.0143-0.01210.2046-0.03840.2437-16.7578-5.4333-7.2246
83.5164-0.19461.05022.33931.84545.0428-0.0717-0.03930.18920.0319-0.0415-0.0513-0.0264-0.00290.130.14610.01140.03280.12350.00110.1593-20.9408-1.1514-14.474
94.6136-0.7767-0.36760.6625-0.06210.9747-0.01730.60530.3351-0.09340.0298-0.0941-0.09830.0515-0.02890.2606-0.0320.05050.2668-0.00970.19-29.57284.9452-20.4071
103.3691-0.81550.45113.90031.72934.49460.02130.8691-0.1222-0.881-0.02310.0151-0.23870.11590.03380.29540.00050.05170.4547-0.05660.2766-34.97211.776-23.7875
115.1229-0.7615-0.02712.0223-0.21154.4553-0.1067-0.1498-0.05340.28730.11050.25320.13190.18850.01290.1797-0.01280.01460.2119-0.04850.1894-37.44613.1709-8.8473
126.13250.4472-0.14074.4597-2.01527.6465-0.0618-0.4746-0.62440.18950.134-0.28120.19570.19720.02590.13950.0011-0.01050.1976-0.00190.2097-45.7711-2.496-9.0509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 161 )
2X-RAY DIFFRACTION2chain 'A' and (resid 162 through 314 )
3X-RAY DIFFRACTION3chain 'B' and (resid 6 through 161 )
4X-RAY DIFFRACTION4chain 'B' and (resid 162 through 314 )
5X-RAY DIFFRACTION5chain 'C' and (resid 6 through 26 )
6X-RAY DIFFRACTION6chain 'C' and (resid 27 through 67 )
7X-RAY DIFFRACTION7chain 'C' and (resid 68 through 111 )
8X-RAY DIFFRACTION8chain 'C' and (resid 112 through 161 )
9X-RAY DIFFRACTION9chain 'C' and (resid 162 through 240 )
10X-RAY DIFFRACTION10chain 'C' and (resid 241 through 272 )
11X-RAY DIFFRACTION11chain 'C' and (resid 273 through 297 )
12X-RAY DIFFRACTION12chain 'C' and (resid 298 through 314 )

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