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- PDB-3qfk: 2.05 Angstrom Crystal Structure of Putative 5'-Nucleotidase from ... -

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Basic information

Entry
Database: PDB / ID: 3qfk
Title2.05 Angstrom Crystal Structure of Putative 5'-Nucleotidase from Staphylococcus aureus in complex with alpha-ketoglutarate
ComponentsUncharacterized protein
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Phosphoesterase
Function / homology
Function and homology information


nucleotidase activity / nucleotide catabolic process / outer membrane-bounded periplasmic space / nucleotide binding / metal ion binding
Similarity search - Function
5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 ...5'-nucleotidase; domain 2 / 5'-Nucleotidase, C-terminal domain / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / DI(HYDROXYETHYL)ETHER / Bifunctional metallophosphatase/5'-nucleotidase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsMinasov, G. / Wawrzak, Z. / Krishna, S.N. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Kiryukhina, O. / Bagnoli, F. / Falugi, F. ...Minasov, G. / Wawrzak, Z. / Krishna, S.N. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Kiryukhina, O. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.05 Angstrom Crystal Structure of Putative 5'-Nucleotidase from Staphylococcus aureus in complex with alpha-ketoglutarate.
Authors: Minasov, G. / Wawrzak, Z. / Krishna, S.N. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Kiryukhina, O. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. ...Authors: Minasov, G. / Wawrzak, Z. / Krishna, S.N. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Kiryukhina, O. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1006
Polymers60,6661
Non-polymers4355
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.444, 84.689, 95.966
Angle α, β, γ (deg.)90.00, 116.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uncharacterized protein / Putative 5'-nucleotidase


Mass: 60665.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: NCTC 8325 / Gene: SAOUHSC_00107 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q2G1L5

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Non-polymers , 6 types, 232 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 7.1 mg/mL, 0.25M Sodium chloride, Tris-HCl pH 8.3, Screen: PEGs II (C11), 0.2M Lithium sulfate, 0.1M Tris pH 8.5, 20% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2010 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 40617 / Num. obs: 40617 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 41.8 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.4
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.05 / Num. unique all: 1827 / % possible all: 88.9

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→29.2 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.471 / SU ML: 0.081
Isotropic thermal model: Atomic thermal factors individually refined
Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22146 1928 5 %RANDOM
Rwork0.17323 ---
all0.17557 36636 --
obs0.17557 36636 95.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.413 Å2
Baniso -1Baniso -2Baniso -3
1--2.51 Å20 Å2-2.53 Å2
2--2.37 Å2-0 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4092 0 23 227 4342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224355
X-RAY DIFFRACTIONr_bond_other_d0.0010.022877
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9445928
X-RAY DIFFRACTIONr_angle_other_deg0.81837014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.955537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01324.672229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.20715707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.8531522
X-RAY DIFFRACTIONr_chiral_restr0.0820.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214985
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02911
X-RAY DIFFRACTIONr_mcbond_it1.1011.52631
X-RAY DIFFRACTIONr_mcbond_other0.3131.51062
X-RAY DIFFRACTIONr_mcangle_it1.924289
X-RAY DIFFRACTIONr_scbond_it3.0931724
X-RAY DIFFRACTIONr_scangle_it4.5944.51639
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 115 -
Rwork0.276 2336 -
obs-1928 81.7 %
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)
11.2855-0.1424-0.11760.95460.05321.5153-0.1411-0.05620.16040.05270.0586-0.1247-0.13160.04110.08250.09420.0565-0.01830.05190.01740.122412.386437.609724.2687
21.3204-0.43460.36240.86320.23291.2193-0.0840.1738-0.1561-0.074-0.0168-0.05020.0034-0.05270.10080.1650.02090.03170.1046-0.01390.10351.617430.228710.2043
30.770.315-0.15582.66291.3751.1267-0.05320.1915-0.0088-0.28950.01040.2018-0.0178-0.16090.04280.18330.06070.00040.20330.0420.1278-17.989441.600319.5019
42.0591-0.80530.33364.9493-0.14181.4560.14610.14360.2329-0.1029-0.1473-0.2314-0.03810.11240.00120.1010.10840.0480.13550.06020.1641-12.337458.440721.6549
51.372-0.2715-0.54722.9183-0.85132.27610.01120.06080.01890.0244-0.00260.43140.1046-0.2592-0.00850.07290.06650.0390.13780.00870.1261-21.012946.548928.136
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 263
2X-RAY DIFFRACTION2A265 - 315
3X-RAY DIFFRACTION3A316 - 379
4X-RAY DIFFRACTION4A380 - 440
5X-RAY DIFFRACTION5A441 - 511

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