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- PDB-5zix: Crystal structure of Ketopantoate reductase from Pseudomonas aeru... -

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Basic information

Entry
Database: PDB / ID: 5zix
TitleCrystal structure of Ketopantoate reductase from Pseudomonas aeruginosa bound to NADP+
ComponentsProbable 2-dehydropantoate 2-reductase
KeywordsOXIDOREDUCTASE / 2-dehydropantoate 2-reductase / panthothenate biosythesis pathway / NADP+ / NADPH
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2-dehydropantoate 2-reductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsKhanppnavar, B. / Datta, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science and TechnologySB/SO/BB-36/2014 India
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2019
Title: Genome-wide survey and crystallographic analysis suggests a role for both horizontal gene transfer and duplication in pantothenate biosynthesis pathways.
Authors: Khanppnavar, B. / Chatterjee, R. / Choudhury, G.B. / Datta, S.
History
DepositionMar 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)101,0808
Polymers99,3173
Non-polymers1,7635
Water5,927329
1
A: Probable 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1255
Polymers33,1061
Non-polymers1,0204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-0 kcal/mol
Surface area13740 Å2
MethodPISA
2
B: Probable 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8492
Polymers33,1061
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-1 kcal/mol
Surface area13430 Å2
MethodPISA
3
C: Probable 2-dehydropantoate 2-reductase


Theoretical massNumber of molelcules
Total (without water)33,1061
Polymers33,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.873, 130.873, 155.296
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-612-

HOH

21B-623-

HOH

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Components

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


Mass: 33105.621 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: panE, PA4397 / Production host: Escherichia coli (E. coli) / 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 3.41 Å3/Da / Density % sol: 63.91 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion / pH: 7.5
Details: 1.3M Sodium-Potassium-Tartarate, 50mM BICINE pH 7.5
PH range: 7.0-8.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97949 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.56→48.15 Å / Num. obs: 44028 / % possible obs: 98.9 % / Redundancy: 14.7 % / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.02 / Rrim(I) all: 0.078 / Net I/σ(I): 31
Reflection shellResolution: 2.56→2.6 Å / Redundancy: 15 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1735 / CC1/2: 0.737 / Rpim(I) all: 0.504 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KS9
Resolution: 2.57→40.598 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 26.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 1224 2.97 %
Rwork0.2117 --
obs0.2129 41248 94.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.57→40.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6984 0 114 329 7427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027238
X-RAY DIFFRACTIONf_angle_d0.4339829
X-RAY DIFFRACTIONf_dihedral_angle_d13.1462712
X-RAY DIFFRACTIONf_chiral_restr0.0341077
X-RAY DIFFRACTIONf_plane_restr0.0031334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5697-2.67260.35341250.34263991X-RAY DIFFRACTION87
2.6726-2.79420.38481270.30564103X-RAY DIFFRACTION89
2.7942-2.94150.29161290.28524276X-RAY DIFFRACTION93
2.9415-3.12570.30661360.25984406X-RAY DIFFRACTION95
3.1257-3.3670.27821420.23664452X-RAY DIFFRACTION96
3.367-3.70560.27761360.20774531X-RAY DIFFRACTION97
3.7056-4.24130.21171370.17654627X-RAY DIFFRACTION98
4.2413-5.34170.18921430.15954712X-RAY DIFFRACTION99
5.3417-40.60310.21481490.18424926X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 32.7224 Å / Origin y: 53.6557 Å / Origin z: 21.706 Å
111213212223313233
T0.2227 Å2-0.0224 Å2-0.0067 Å2-0.3392 Å2-0.0243 Å2--0.1802 Å2
L1.6525 °2-0.1221 °2-0.2052 °2-0.4293 °20.0991 °2--0.2567 °2
S0.0453 Å °-0.157 Å °0.1517 Å °0.0248 Å °0.0193 Å °-0.0121 Å °0.0052 Å °0.0571 Å °-0.0598 Å °
Refinement TLS groupSelection details: all

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