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- PDB-3g17: Structure of putative 2-dehydropantoate 2-reductase from staphylo... -

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Basic information

Entry
Database: PDB / ID: 3g17
TitleStructure of putative 2-dehydropantoate 2-reductase from staphylococcus aureus
ComponentsSimilar to 2-dehydropantoate 2-reductase
Keywordsstructural genomics / unknown function / Putative 2-dehydropantoate 2-reductase / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase activity / phosphogluconate dehydrogenase (decarboxylating) activity / pantothenate biosynthetic process / 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
2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Structure of putative 2-dehydropantoate 2-reductase from staphylococcus aureus
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionJan 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Similar to 2-dehydropantoate 2-reductase
B: Similar to 2-dehydropantoate 2-reductase
C: Similar to 2-dehydropantoate 2-reductase
D: Similar to 2-dehydropantoate 2-reductase
E: Similar to 2-dehydropantoate 2-reductase
F: Similar to 2-dehydropantoate 2-reductase
G: Similar to 2-dehydropantoate 2-reductase
H: Similar to 2-dehydropantoate 2-reductase


Theoretical massNumber of molelcules
Total (without water)267,4888
Polymers267,4888
Non-polymers00
Water7,134396
1
A: Similar to 2-dehydropantoate 2-reductase
E: Similar to 2-dehydropantoate 2-reductase


Theoretical massNumber of molelcules
Total (without water)66,8722
Polymers66,8722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-13 kcal/mol
Surface area25130 Å2
MethodPISA
2
B: Similar to 2-dehydropantoate 2-reductase
F: Similar to 2-dehydropantoate 2-reductase


Theoretical massNumber of molelcules
Total (without water)66,8722
Polymers66,8722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-12 kcal/mol
Surface area24920 Å2
MethodPISA
3
C: Similar to 2-dehydropantoate 2-reductase
H: Similar to 2-dehydropantoate 2-reductase


Theoretical massNumber of molelcules
Total (without water)66,8722
Polymers66,8722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-12 kcal/mol
Surface area25120 Å2
MethodPISA
4
D: Similar to 2-dehydropantoate 2-reductase
G: Similar to 2-dehydropantoate 2-reductase


Theoretical massNumber of molelcules
Total (without water)66,8722
Polymers66,8722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-13 kcal/mol
Surface area25360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.239, 99.640, 100.261
Angle α, β, γ (deg.)103.660, 105.230, 102.260
Int Tables number1
Space group name H-MP1
Detailsauthors states biological unit is unknown

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Components

#1: Protein
Similar to 2-dehydropantoate 2-reductase


Mass: 33435.938 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / Gene: SAV2600 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99R37, UniProt: A0A0H3K174*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-tris pH 6.5, 10% PEG 10K, 0.2M 0.1M Ammonium Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 113899 / % possible obs: 98.6 % / Redundancy: 5 % / Rmerge(I) obs: 0.104 / Χ2: 1.197 / Net I/σ(I): 16.202
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3850.587113310.982197.8
2.38-2.4850.483112590.988197.8
2.48-2.5950.369113661.006198.1
2.59-2.7350.289113151.038198.2
2.73-2.950.207114151.111198.5
2.9-3.1250.146113871.198198.6
3.12-3.4450.105114051.286198.8
3.44-3.934.90.079114471.329199.1
3.93-4.954.80.066114761.35199.3
4.95-505.10.064114981.672199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
PHENIXphasing
RefinementResolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.198 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.808 / SU B: 7.534 / SU ML: 0.185 / SU R Cruickshank DPI: 0.352 / SU Rfree: 0.254 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.352 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26 5744 5 %RANDOM
Rwork0.2 ---
obs0.203 113884 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.18 Å2 / Biso mean: 36.966 Å2 / Biso min: 14.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20.25 Å20.72 Å2
2--0.99 Å20.41 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18282 0 0 396 18678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02218674
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.94225458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89752288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.16224.434918
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.132153083
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.90515104
X-RAY DIFFRACTIONr_chiral_restr0.0960.22965
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114205
X-RAY DIFFRACTIONr_mcbond_it0.7141.511412
X-RAY DIFFRACTIONr_mcangle_it1.378218583
X-RAY DIFFRACTIONr_scbond_it2.03737262
X-RAY DIFFRACTIONr_scangle_it3.3634.56873
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 404 -
Rwork0.252 7526 -
all-7930 -
obs--92.23 %

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