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- PDB-4py9: Crystal structure of an exopolyphosphatase-related protein from B... -

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Basic information

Entry
Database: PDB / ID: 4py9
TitleCrystal structure of an exopolyphosphatase-related protein from Bacteroides Fragilis. Northeast Structural Genomics target BFR192
ComponentsPutative exopolyphosphatase-related protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / EXOPOLYPHOSPHATASE-RELATED PROTEIN
Function / homology
Function and homology information


nucleic acid binding
Similarity search - Function
Diaminopimelate Epimerase; Chain A, domain 1 - #30 / inorganic pyrophosphatase (n-terminal core) / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Putative exopolyphosphatase-related protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsSeetharaman, J. / Abashidze, M. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. ...Seetharaman, J. / Abashidze, M. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of an exopolyphosphatase-related protein from Bacteroides Fragilis. Northeast Structural Genomics target BFR192
Authors: Seetharaman, J. / Abashidze, M. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast ...Authors: Seetharaman, J. / Abashidze, M. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
History
DepositionMar 26, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionJun 25, 2014ID: 3DMA
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative exopolyphosphatase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2449
Polymers39,7721
Non-polymers4728
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative exopolyphosphatase-related protein
hetero molecules

A: Putative exopolyphosphatase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,48718
Polymers79,5432
Non-polymers94416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area5840 Å2
ΔGint-123 kcal/mol
Surface area29720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.892, 90.892, 107.684
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative exopolyphosphatase-related protein


Mass: 39771.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: BF3900 / Plasmid: PET 21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q64PD9
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 320 MM KACETATE, 100 MM NAACETATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 4, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 47146 / Num. obs: 40928 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Rmerge(I) obs: 0.074 / Rsym value: 0.056 / Net I/σ(I): 17.3
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 17 / Rsym value: 0.28 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.25→45.45 Å / SU B: 6.366 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.312 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26354 2105 9.3 %RANDOM
Rwork0.23149 ---
obs0.23457 20515 90.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.288 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å21.65 Å2-0 Å2
2--1.65 Å2-0 Å2
3----5.34 Å2
Refinement stepCycle: LAST / Resolution: 2.25→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 24 109 2858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192799
X-RAY DIFFRACTIONr_bond_other_d0.0010.022633
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.9813771
X-RAY DIFFRACTIONr_angle_other_deg0.68836081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1355338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75724.154130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11815471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9851514
X-RAY DIFFRACTIONr_chiral_restr0.0530.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023107
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02639
LS refinement shellResolution: 2.252→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 133 -
Rwork0.264 1304 -
obs--79.52 %

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