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- PDB-2qb8: Saccharomyces cerevisiae cytosolic exopolyphosphatase, ATP complex -

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Basic information

Entry
Database: PDB / ID: 2qb8
TitleSaccharomyces cerevisiae cytosolic exopolyphosphatase, ATP complex
ComponentsExopolyphosphatase
KeywordsHYDROLASE / a/b/a structure / DHH family phosphatase
Function / homology
Function and homology information


polyphosphate catabolic process / exopolyphosphatase / exopolyphosphatase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
DHHA2 domain / DHHA2 domain / DHHA2 domain superfamily / DHHA2 domain / DHHA2 / inorganic pyrophosphatase (n-terminal core) / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family / DHH phosphoesterase superfamily ...DHHA2 domain / DHHA2 domain / DHHA2 domain superfamily / DHHA2 domain / DHHA2 / inorganic pyrophosphatase (n-terminal core) / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family / DHH phosphoesterase superfamily / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Polyphosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWhite, S.A. / Ugochukwu, E.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The crystal structure of the cytosolic exopolyphosphatase from Saccharomyces cerevisiae reveals the basis for substrate specificity.
Authors: Ugochukwu, E. / Lovering, A.L. / Mather, O.C. / Young, T.W. / White, S.A.
History
DepositionJun 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN THE TITLE OF THIS DEPOSITION STATES THAT THIS IS AN ATP COMPLEX. AUTHORS DID NOT PROVIDE ...HETEROGEN THE TITLE OF THIS DEPOSITION STATES THAT THIS IS AN ATP COMPLEX. AUTHORS DID NOT PROVIDE INFORMATION REGARDING THE MISSING ATOMS OF THIS LIGAND. THIS ENTRY HAS BEEN RELEASED WITHOUT DEPOSITOR'S CHECKING AND CORRECTIONS, ONLY WITH NECESSARY PDB STAFF INTERVENTION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exopolyphosphatase
B: Exopolyphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7745
Polymers90,2192
Non-polymers5563
Water11,584643
1
A: Exopolyphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6413
Polymers45,1091
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exopolyphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1342
Polymers45,1091
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.134, 82.847, 121.761
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Exopolyphosphatase / ExopolyPase / Metaphosphatase


Mass: 45109.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: PPX1, YHR201C / Plasmid: pET11c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38698, exopolyphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / 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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 7% PEG 4000, 150 mM Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→30.5 Å / Num. obs: 60043 / % possible obs: 99.4 % / Redundancy: 4 % / Rsym value: 0.065 / Net I/σ(I): 7.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 8715 / Rsym value: 0.327 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QB6

2qb6


Resolution: 1.9→30.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.253 / SU ML: 0.099 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23287 3122 5 %RANDOM
Rwork0.18389 ---
obs0.18633 59362 99.25 %-
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: 26 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2---0.41 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6286 0 14 643 6943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0216398
X-RAY DIFFRACTIONr_bond_other_d0.0020.025856
X-RAY DIFFRACTIONr_angle_refined_deg1.151.9698612
X-RAY DIFFRACTIONr_angle_other_deg1.137313708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.635781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2964
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027024
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021242
X-RAY DIFFRACTIONr_nbd_refined0.2030.21407
X-RAY DIFFRACTIONr_nbd_other0.2270.26848
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.23793
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2525
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined1.9540.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6631.53888
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23626289
X-RAY DIFFRACTIONr_scbond_it1.68332510
X-RAY DIFFRACTIONr_scangle_it2.8784.52321
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.255 237
Rwork0.203 4327

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