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- PDB-8ixm: Pseudomoans Aerugiona Wildtype Ketopantoate Reductase ternary com... -

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Basic information

Entry
Database: PDB / ID: 8ixm
TitlePseudomoans Aerugiona Wildtype Ketopantoate Reductase ternary complex with NADP+ and alpha-Ketoisocaproic acid
Components2-dehydropantoate 2-reductase
KeywordsOXIDOREDUCTASE / PanE2 / ternary complex / Ketopantoate Reductase / alpha-Ketoisocaproic acid
Function / homology2-OXO-4-METHYLPENTANOIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsChoudhury, G.B. / Datta, S.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: To Be Published
Title: KEtopantoate reductase of Pseudomonas
Authors: Choudhury, G.B. / Dutta, S.
History
DepositionApr 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4578
Polymers68,4102
Non-polymers2,0466
Water7,530418
1
A: 2-dehydropantoate 2-reductase
hetero molecules

B: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4578
Polymers68,4102
Non-polymers2,0466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area6120 Å2
ΔGint-2 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.587, 46.769, 95.775
Angle α, β, γ (deg.)90.00, 98.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 2-dehydropantoate 2-reductase


Mass: 34205.191 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 424 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-COI / 2-OXO-4-METHYLPENTANOIC ACID / alpha-ketoisocaproic acid


Mass: 130.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 16% PEG 8000, 100mM CHES 9.5

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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: Mar 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.96→23.42 Å / Num. obs: 42331 / % possible obs: 99.7 % / Redundancy: 9.1 % / CC1/2: 0.998 / Net I/σ(I): 12
Reflection shellResolution: 1.96→2.03 Å / Num. unique obs: 4206 / CC1/2: 0.547

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→23.416 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2375 3516 4.28 %
Rwork0.192 --
obs0.194 42230 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→23.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4715 0 133 418 5266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034980
X-RAY DIFFRACTIONf_angle_d0.6166773
X-RAY DIFFRACTIONf_dihedral_angle_d6.5723453
X-RAY DIFFRACTIONf_chiral_restr0.038727
X-RAY DIFFRACTIONf_plane_restr0.004885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.98680.36831440.33443146X-RAY DIFFRACTION100
1.9868-2.01520.3841390.33183178X-RAY DIFFRACTION100
2.0152-2.04530.36571400.31283157X-RAY DIFFRACTION100
2.0453-2.07720.30771350.28983129X-RAY DIFFRACTION100
2.0772-2.11130.31941390.26913083X-RAY DIFFRACTION100
2.1113-2.14760.25121430.24573190X-RAY DIFFRACTION100
2.1476-2.18670.28281390.23573126X-RAY DIFFRACTION100
2.1867-2.22870.24691440.22913192X-RAY DIFFRACTION100
2.2287-2.27410.31641370.23243112X-RAY DIFFRACTION100
2.2741-2.32350.28871400.22243159X-RAY DIFFRACTION100
2.3235-2.37750.27811400.21233093X-RAY DIFFRACTION100
2.3775-2.43690.25491420.21223155X-RAY DIFFRACTION100
2.4369-2.50280.22341420.19463126X-RAY DIFFRACTION100
2.5028-2.57630.2321430.19773169X-RAY DIFFRACTION100
2.5763-2.65940.30721390.2033149X-RAY DIFFRACTION100
2.6594-2.75430.25481440.19473155X-RAY DIFFRACTION100
2.7543-2.86440.26571360.19583119X-RAY DIFFRACTION100
2.8644-2.99450.23291400.19363134X-RAY DIFFRACTION100
2.9945-3.1520.20961460.19083165X-RAY DIFFRACTION100
3.152-3.34890.24161450.18243141X-RAY DIFFRACTION100
3.3489-3.60670.22651420.16593165X-RAY DIFFRACTION100
3.6067-3.9680.18661400.14713113X-RAY DIFFRACTION100
3.968-4.53860.20321420.1353136X-RAY DIFFRACTION100
4.5386-5.70450.19431390.14253154X-RAY DIFFRACTION100
5.7045-23.4160.13691360.143127X-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)
11.605-1.6977-0.29371.9287-0.41884.6057-0.1854-0.44760.7080.3968-0.0132-0.4291-0.56650.2343-0.5360.37840.15-0.16480.2694-0.23890.377522.30524.249634.458
21.2197-0.33960.43250.6435-0.0880.4545-0.1988-0.3110.60020.45860.1608-0.30190.08530.3069-0.0840.29450.2-0.08860.3162-0.20740.36424.763-1.141732.7182
32.2246-1.07360.14290.94320.32950.56290.03090.0463-0.06790.15030.0389-0.02550.26890.208-0.07560.27720.2355-0.06640.3067-0.05140.192220.5358-8.480928.8219
40.5887-0.05350.07960.73710.65122.4894-0.1109-0.299-0.17480.46450.19140.20250.2847-0.4401-0.04320.2610.08830.0460.2840.05060.187610.5413-12.979720.5607
58.7835-2.485-1.85710.79490.88171.7947-0.0588-0.0350.8642-0.0220.109-0.0439-0.41460.0015-0.16480.29360.119-0.05390.1959-0.02620.250514.18941.370314.3102
62.5681.18220.21274.81370.72682.7975-0.0344-0.1329-0.16620.33670.3228-0.30410.35940.2679-0.1930.17490.1052-0.00810.2185-0.06090.1122.0944-15.799412.0493
71.4821.3681.09511.4611.13271.9506-0.21150.437-0.0111-0.15560.3016-0.15830.02960.4967-0.22690.05170.07780.00080.29630.00330.095922.949-9.3663.437
81.8381-0.89760.57981.43460.86272.1036-0.367-0.4611.0207-0.22150.1143-0.4578-0.8984-0.096-0.36630.36820.1535-0.020.1952-0.17910.3599-11.093226.276734.198
91.64210.00680.07670.47070.57422.5982-0.0428-0.23230.04180.07580.07740.00660.0118-0.4782-0.01780.14050.06520.02190.13930.00990.1537-14.875511.489824.4226
102.1943-0.14730.26821.64380.69572.5067-0.2251-0.088-0.01690.35630.31820.3896-0.1383-0.4176-0.03120.1850.08070.04650.18180.05750.1473-14.794512.339311.3112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 111 )
3X-RAY DIFFRACTION3chain 'A' and (resid 112 through 161 )
4X-RAY DIFFRACTION4chain 'A' and (resid 162 through 258 )
5X-RAY DIFFRACTION5chain 'A' and (resid 259 through 273 )
6X-RAY DIFFRACTION6chain 'A' and (resid 274 through 297 )
7X-RAY DIFFRACTION7chain 'A' and (resid 298 through 314 )
8X-RAY DIFFRACTION8chain 'B' and (resid 5 through 96 )
9X-RAY DIFFRACTION9chain 'B' and (resid 97 through 240 )
10X-RAY DIFFRACTION10chain 'B' and (resid 241 through 314 )

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