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

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Basic information

Entry
Database: PDB / ID: 5zik
TitleCrystal structure of Ketopantoate reductase from Pseudomonas aeruginosa
ComponentsProbable 2-dehydropantoate 2-reductase
KeywordsOXIDOREDUCTASE / 2-dehydropantoate 2-reductase / panthothenate biosythesis pathway / ApbA family / Rossman fold
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
2-dehydropantoate 2-reductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 16, 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 1.3Dec 25, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.4Nov 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)99,7938
Polymers99,3173
Non-polymers4765
Water4,342241
1
A: Probable 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3904
Polymers33,1061
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14160 Å2
MethodPISA
2
B: Probable 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2983
Polymers33,1061
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-18 kcal/mol
Surface area14060 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 area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.310, 131.310, 156.848
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-578-

HOH

21C-457-

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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 8
Details: 1.1M Sodium-Potassium-Tartarate, 50mM BICINE pH 8.0
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: 2.45→47.01 Å / Num. obs: 51232 / % possible obs: 99.7 % / Redundancy: 10 % / Biso Wilson estimate: 51.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.024 / Net I/σ(I): 24.5
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5014 / CC1/2: 0.837 / Rpim(I) all: 0.394 / % 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

1ks9


Resolution: 2.45→36.123 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.02
RfactorNum. reflection% reflection
Rfree0.2536 1406 2.89 %
Rwork0.2236 --
obs0.2244 48641 95.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→36.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6984 0 26 241 7251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027152
X-RAY DIFFRACTIONf_angle_d0.4449700
X-RAY DIFFRACTIONf_dihedral_angle_d14.0464277
X-RAY DIFFRACTIONf_chiral_restr0.0351060
X-RAY DIFFRACTIONf_plane_restr0.0031287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.53760.41981290.34854380X-RAY DIFFRACTION90
2.5376-2.63910.3941290.33724463X-RAY DIFFRACTION92
2.6391-2.75920.39921300.3394406X-RAY DIFFRACTION90
2.7592-2.90460.41410.30734644X-RAY DIFFRACTION95
2.9046-3.08650.33111400.28514703X-RAY DIFFRACTION96
3.0865-3.32470.28221440.25414777X-RAY DIFFRACTION97
3.3247-3.65890.24031440.22154781X-RAY DIFFRACTION97
3.6589-4.18770.23741440.19464875X-RAY DIFFRACTION98
4.1877-5.27350.20321490.17044999X-RAY DIFFRACTION99
5.2735-36.12670.18931560.1945207X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 33.2456 Å / Origin y: 53.8235 Å / Origin z: 21.9062 Å
111213212223313233
T0.3019 Å2-0.0338 Å2-0.0185 Å2-0.374 Å20.0215 Å2--0.478 Å2
L1.3661 °2-0.0704 °2-0.1694 °2-0.3608 °20.1403 °2--0.3296 °2
S0.0378 Å °-0.1425 Å °0.0747 Å °0.0345 Å °0.0171 Å °0.0254 Å °0.0326 Å °0.0038 Å °-0.0544 Å °
Refinement TLS groupSelection details: all

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