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- PDB-4yca: Evidence of Kinetic Cooperativity in dimeric Ketopantoate Reducta... -

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Basic information

Entry
Database: PDB / ID: 4yca
TitleEvidence of Kinetic Cooperativity in dimeric Ketopantoate Reductase from Staphylococcus aureus
Components2-dehydropantoate 2-reductase
KeywordsOXIDOREDUCTASE / Reductase / Dimer / Rossmann / kinetic cooperativity
Function / homology
Function and homology information


2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase activity / phosphogluconate dehydrogenase (decarboxylating) activity / pantothenate biosynthetic process / nucleotide 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 ...: / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / 2-dehydropantoate 2-reductase / :
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsSanchez, J.E. / Gross, P.G. / Goetze, R. / Walsh Jr., R.M. / Peeples, W.B. / Wood, Z.A.
CitationJournal: Biochemistry / Year: 2015
Title: Evidence of Kinetic Cooperativity in Dimeric Ketopantoate Reductase from Staphylococcus aureus.
Authors: Sanchez, J.E. / Gross, P.G. / Goetze, R.W. / Walsh Jr., R.M. / Peeples, W.B. / Wood, Z.A.
History
DepositionFeb 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3Jul 20, 2016Group: Data collection
Revision 1.4May 2, 2018Group: Data collection / Database references / Derived calculations
Category: citation_author / pdbx_struct_oper_list
Item: _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Sep 27, 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

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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)68,3634
Polymers66,8722
Non-polymers1,4912
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-17 kcal/mol
Surface area24200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.180, 85.210, 177.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 2-dehydropantoate 2-reductase


Mass: 33435.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: CH52_06005, DA92_02185 / Production host: Escherichia coli (E. coli)
References: UniProt: W8TQG0, UniProt: A0A0J9X283*PLUS, 2-dehydropantoate 2-reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 4mM KP, 4mM NADP+, 300mM Magnesium acetate, 100mM MES, 15% PEG 3,350

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→44.3 Å / Num. obs: 59348 / % possible obs: 99.9 % / Redundancy: 13.8 % / Net I/σ(I): 1.34

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G17

3g17


Resolution: 1.81→44.3 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 2086 3.49 %
Rwork0.1726 --
obs0.1739 59348 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4551 0 96 411 5058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084860
X-RAY DIFFRACTIONf_angle_d1.0726671
X-RAY DIFFRACTIONf_dihedral_angle_d16.5481812
X-RAY DIFFRACTIONf_chiral_restr0.047777
X-RAY DIFFRACTIONf_plane_restr0.004850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.84510.3611350.32923725X-RAY DIFFRACTION97
1.8451-1.89130.27831370.25633779X-RAY DIFFRACTION100
1.8913-1.94240.26761360.24493806X-RAY DIFFRACTION100
1.9424-1.99960.25451380.22663803X-RAY DIFFRACTION100
1.9996-2.06410.26111370.19953793X-RAY DIFFRACTION100
2.0641-2.13790.21551380.193826X-RAY DIFFRACTION100
2.1379-2.22350.24491390.17563836X-RAY DIFFRACTION100
2.2235-2.32470.2221370.16393798X-RAY DIFFRACTION100
2.3247-2.44720.19111380.17263838X-RAY DIFFRACTION100
2.4472-2.60050.20281380.16673833X-RAY DIFFRACTION100
2.6005-2.80130.24191410.17173882X-RAY DIFFRACTION100
2.8013-3.08310.22251390.17693864X-RAY DIFFRACTION100
3.0831-3.52910.20531420.16153912X-RAY DIFFRACTION100
3.5291-4.44560.17271410.13723927X-RAY DIFFRACTION100
4.4456-44.30.17421500.15234136X-RAY DIFFRACTION100

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