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- PDB-2flo: Crystal structure of exopolyphosphatase (PPX) from E. coli O157:H7 -

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Basic information

Entry
Database: PDB / ID: 2flo
TitleCrystal structure of exopolyphosphatase (PPX) from E. coli O157:H7
ComponentsExopolyphosphatase
KeywordsHYDROLASE / exopolyphosphatase / PPX/GPPA / metaphosphatase / Structural Genomics / Bacterial Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


phosphorus metabolic process / exopolyphosphatase / exopolyphosphatase activity / plasma membrane
Similarity search - Function
Alpha-Beta Plaits - #2260 / Exopolyphosphatase / Pyrophosphatase, GppA/Ppx-type / Ppx/GppA phosphatase / Ppx/GppA phosphatase family / Exopolyphosphatase. Domain 2 / Hypothetical protein af1432 / Hypothetical protein af1432 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain ...Alpha-Beta Plaits - #2260 / Exopolyphosphatase / Pyrophosphatase, GppA/Ppx-type / Ppx/GppA phosphatase / Ppx/GppA phosphatase family / Exopolyphosphatase. Domain 2 / Hypothetical protein af1432 / Hypothetical protein af1432 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRangarajan, E.S. / Cygler, M. / Matte, A. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The Structure of the Exopolyphosphatase (PPX) from Escherichia coli O157:H7 Suggests a Binding Mode for Long Polyphosphate Chains.
Authors: Rangarajan, E.S. / Nadeau, G. / Li, Y. / Wagner, J. / Hung, M.N. / Schrag, J.D. / Cygler, M. / Matte, A.
History
DepositionJan 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exopolyphosphatase
B: Exopolyphosphatase
C: Exopolyphosphatase
D: Exopolyphosphatase


Theoretical massNumber of molelcules
Total (without water)240,8534
Polymers240,8534
Non-polymers00
Water11,349630
1
A: Exopolyphosphatase
B: Exopolyphosphatase


Theoretical massNumber of molelcules
Total (without water)120,4272
Polymers120,4272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Exopolyphosphatase
D: Exopolyphosphatase


Theoretical massNumber of molelcules
Total (without water)120,4272
Polymers120,4272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.547, 132.139, 107.850
Angle α, β, γ (deg.)90.00, 105.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Exopolyphosphatase / ExopolyPase / Metaphosphatase


Mass: 60213.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: ppx / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFL8, exopolyphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 5% PEG350, 0.1M Na Citrate (pH 4.6) and 5% MPD., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X8C10.9801
SYNCHROTRONNSLS X29A21.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDSep 5, 2005
ADSC QUANTUM 42CCDOct 2, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SiliconeSINGLE WAVELENGTHMx-ray1
2SiliconeSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.98011
21.11
ReflectionResolution: 2.04→104.257 Å / Num. all: 128211 / Num. obs: 119378 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 31.1 Å2 / Rsym value: 0.073 / Net I/σ(I): 9.2
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 1.9 % / Num. unique all: 5533 / Rsym value: 0.405 / % possible all: 33.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Map obtained from peak wavelength used for orientation corresponding to the present dataset.

Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.57 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.248 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2471 6490 5.1 %RANDOM
Rwork0.20248 ---
all0.2047 128211 --
obs0.20477 121721 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.081 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å2-1.26 Å2
2--1.39 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15835 0 0 630 16465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02216160
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.95821821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56251979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34423.545787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.159152935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5615148
X-RAY DIFFRACTIONr_chiral_restr0.0930.22415
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212200
X-RAY DIFFRACTIONr_nbd_refined0.2040.27464
X-RAY DIFFRACTIONr_nbtor_refined0.3010.211020
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2792
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.24
X-RAY DIFFRACTIONr_mcbond_it0.8841.510234
X-RAY DIFFRACTIONr_mcangle_it1.381215813
X-RAY DIFFRACTIONr_scbond_it2.18536752
X-RAY DIFFRACTIONr_scangle_it3.4934.56008
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 390 -
Rwork0.243 7492 -
obs--82.04 %

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