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- PDB-6k1r: Crystal structure of Ketopantoate reductase from Pseudomonas aeru... -

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Basic information

Entry
Database: PDB / ID: 6k1r
TitleCrystal structure of Ketopantoate reductase from Pseudomonas aeruginosa in complex with NAD+ and ketopantoate
ComponentsProbable 2-dehydropantoate 2-reductase
KeywordsOXIDOREDUCTASE / Vitamin B5 biosynthesis pathway / Redox cofactor
Function / homology
Function and homology information


2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase activity / pantothenate biosynthetic process / NADP binding / cytoplasm
Similarity search - Function
Ketopantoate reductase ApbA/PanE / Ketopantoate reductase, C-terminal domain / Ketopantoate reductase PanE/ApbA C terminal / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily ...Ketopantoate reductase ApbA/PanE / Ketopantoate reductase, C-terminal domain / Ketopantoate reductase PanE/ApbA C terminal / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
KETOPANTOATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2-dehydropantoate 2-reductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsKhanppnavar, B. / Choudhury, A. / Datta, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (India)SB/SO/BB - 36/2014 India
CitationJournal: Biochimie / Year: 2021
Title: Crystallographic and biophysical analyses of Pseudomonas aeruginosa ketopantoate reductase: Implications of ligand induced conformational changes in cofactor recognition.
Authors: Choudhury, A. / Khanppnavar, B. / Datta, S.
History
DepositionMay 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author / database_2
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.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)107,78010
Polymers105,8313
Non-polymers1,9497
Water5,080282
1
A: Probable 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2715
Polymers35,2771
Non-polymers9944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-3 kcal/mol
Surface area13690 Å2
MethodPISA
2
B: Probable 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0873
Polymers35,2771
Non-polymers8102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-3 kcal/mol
Surface area13650 Å2
MethodPISA
3
C: Probable 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4232
Polymers35,2771
Non-polymers1461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.995, 129.995, 155.105
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-564-

HOH

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Components

#1: Protein Probable 2-dehydropantoate 2-reductase / Ketopantoate reductase / KPR


Mass: 35276.977 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: panE / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9HW09, 2-dehydropantoate 2-reductase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#3: Chemical ChemComp-KPL / KETOPANTOATE / 2-DEHYDROPANTOATE / Ketopantoic acid


Mass: 146.141 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H10O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

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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: 3.35 Å3/Da / Density % sol: 63.33 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 7.5
Details: 1.3M Sodium-Potassium-Tartarate, 50mM BICINE pH 7.5, 20 mM NAD+
PH range: 7.0-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.5 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.55→23.46 Å / Num. obs: 104626 / % possible obs: 100 % / Redundancy: 28.4 % / Net I/σ(I): 18.1
Reflection shellResolution: 2.55→2.64 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4295 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: 000)refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZIK

5zik


Resolution: 2.55→22.98 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.07
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER F_MINUS AND F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2689 3070 3.79 %
Rwork0.244 --
obs0.245 81035 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→22.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7032 0 130 282 7444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027337
X-RAY DIFFRACTIONf_angle_d0.639969
X-RAY DIFFRACTIONf_dihedral_angle_d15.384335
X-RAY DIFFRACTIONf_chiral_restr0.0361084
X-RAY DIFFRACTIONf_plane_restr0.0031314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.58980.37441320.33123530X-RAY DIFFRACTION97
2.5898-2.63220.43531380.31553499X-RAY DIFFRACTION98
2.6322-2.67750.37981390.32143524X-RAY DIFFRACTION97
2.6775-2.72610.32711460.31833557X-RAY DIFFRACTION98
2.7261-2.77850.38011320.3153552X-RAY DIFFRACTION98
2.7785-2.83510.32081450.31323531X-RAY DIFFRACTION98
2.8351-2.89660.32571410.31563547X-RAY DIFFRACTION98
2.8966-2.96390.32211300.31593533X-RAY DIFFRACTION97
2.9639-3.03780.40781360.30613477X-RAY DIFFRACTION97
3.0378-3.11980.27221320.29513533X-RAY DIFFRACTION97
3.1198-3.21130.29991430.2813483X-RAY DIFFRACTION97
3.2113-3.31470.32121370.27243477X-RAY DIFFRACTION97
3.3147-3.43280.30411430.25983549X-RAY DIFFRACTION97
3.4328-3.56980.31441400.24633471X-RAY DIFFRACTION97
3.5698-3.73160.25921430.23923578X-RAY DIFFRACTION98
3.7316-3.92740.26841400.22443557X-RAY DIFFRACTION98
3.9274-4.17210.23181430.21173559X-RAY DIFFRACTION99
4.1721-4.4920.22361440.19653623X-RAY DIFFRACTION99
4.492-4.940.19991390.19263580X-RAY DIFFRACTION99
4.94-5.64560.23051400.20373587X-RAY DIFFRACTION99
5.6456-7.07820.21481470.2383615X-RAY DIFFRACTION100
7.0782-22.9810.19181400.18863603X-RAY DIFFRACTION100

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