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- PDB-4s3m: Evidence of kinetic cooperativity in dimeric Ketopantoate Reducta... -

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Basic information

Entry
Database: PDB / ID: 4s3m
TitleEvidence of kinetic cooperativity in dimeric Ketopantoate Reductase from Staphylococcus aureus
Components2-dehydropantoate 2-reductase
KeywordsOXIDOREDUCTASE / Rossman Fold / Nucleotide binding domain / NADPH / Oxidation
Function / homology
Function and homology information


2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase activity / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / pantothenate biosynthetic process / nucleotide binding
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 Rossmann-like Domain ...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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 6-phosphogluconate dehydrogenase, decarboxylating / 2-dehydropantoate 2-reductase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSanchez, J.E. / Walsh Jr., R.M. / 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 1.1Jun 10, 2015Group: Database references
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)68,4434
Polymers66,9562
Non-polymers1,4872
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 2-dehydropantoate 2-reductase
hetero molecules

B: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4434
Polymers66,9562
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555x+1/2,y+1/2,z+1/21
Buried area4240 Å2
ΔGint-18 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.648, 66.764, 122.378
Angle α, β, γ (deg.)90.00, 110.15, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein 2-dehydropantoate 2-reductase


Mass: 33478.016 Da / Num. of mol.: 2 / Mutation: A181L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: SAV2600 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99R37, UniProt: A0A0J9X201*PLUS, 2-dehydropantoate 2-reductase
#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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 293 K / pH: 6
Details: 4mM NADPH, 5-6% tacsimate, 100mM MES, 15-16% polyethylene glycol 3350, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2012
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→31 Å / Num. obs: 20271 / % possible obs: 99.2 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.72 Å / % possible all: 94.4

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30.97 Å / SU ML: 0.42 / σ(F): 0.86 / Phase error: 29.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 2018 10 %
Rwork0.222 --
obs0.227 20177 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→30.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4200 0 96 42 4338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024375
X-RAY DIFFRACTIONf_angle_d0.6655978
X-RAY DIFFRACTIONf_dihedral_angle_d15.3461596
X-RAY DIFFRACTIONf_chiral_restr0.024709
X-RAY DIFFRACTIONf_plane_restr0.002750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.605-2.66970.37851100.3632996X-RAY DIFFRACTION76
2.6697-2.74180.35721450.33891296X-RAY DIFFRACTION98
2.7418-2.82250.34811490.31571338X-RAY DIFFRACTION100
2.8225-2.91350.3651440.29281304X-RAY DIFFRACTION99
2.9135-3.01760.2941470.2911315X-RAY DIFFRACTION100
3.0176-3.13830.31171440.28391300X-RAY DIFFRACTION100
3.1383-3.28090.34571480.25541331X-RAY DIFFRACTION99
3.2809-3.45370.30751450.2391310X-RAY DIFFRACTION99
3.4537-3.66980.27421480.22891329X-RAY DIFFRACTION99
3.6698-3.95260.26141460.2041319X-RAY DIFFRACTION99
3.9526-4.34940.23151470.18761315X-RAY DIFFRACTION99
4.3494-4.97650.20581470.17271330X-RAY DIFFRACTION99
4.9765-6.26140.25461480.19981331X-RAY DIFFRACTION99
6.2614-30.97630.22241500.17181345X-RAY DIFFRACTION97
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)
18.0483-0.98892.14976.3065-2.24225.4509-0.04940.2142-0.1951-0.1519-0.0708-0.4527-0.07420.41150.09860.3623-0.04040.03050.3019-0.05560.257916.91318.943914.0516
27.8432-1.94683.71362.21-2.75637.39140.1679-0.113-0.6145-0.09230.34730.24230.5521-0.4861-0.52370.3687-0.06940.00360.325-0.03320.37437.186213.250315.0006
31.3410.6125-1.75050.9485-1.41042.83820.08120.2790.1196-0.1433-0.0438-0.06050.34530.2136-0.00130.42820.02740.05870.4531-0.04310.425-0.454610.43735.4637
47.18511.11870.20764.82930.24678.76630.30760.62940.7449-0.34590.06820.0279-0.457-0.3776-0.35450.47560.07560.15470.45510.05510.4729-6.362816.266834.2813
57.6544-0.68242.81323.5125-0.11224.61790.08040.1266-0.59660.2985-0.10140.1178-0.1405-0.21690.00450.409-0.095-0.03180.5082-0.09790.3868-19.9671-13.892623.7068
64.4492-1.6071-0.96282.50191.7214.60120.3761-0.52970.8318-0.09590.2734-0.8267-0.56160.8294-0.49970.3983-0.05180.06340.4648-0.17840.5987-29.7611-11.3928-1.0055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 98 )
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 158 )
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 198 )
4X-RAY DIFFRACTION4chain 'A' and (resid 199 through 283 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 161 )
6X-RAY DIFFRACTION6chain 'B' and (resid 162 through 285 )

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