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- PDB-2qb7: Saccharomyces cerevisiae cytosolic exopolyphosphatase, phosphate ... -

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Basic information

Entry
Database: PDB / ID: 2qb7
TitleSaccharomyces cerevisiae cytosolic exopolyphosphatase, phosphate 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, N-terminal domain / 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, N-terminal domain / DHH phosphoesterase superfamily / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / PHOSPHATE ION / Polyphosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 A PHOSPHATE COMPLEX. AUTHORS DID NOT ...HETEROGEN THE TITLE OF THIS DEPOSITION STATES THAT THIS IS A PHOSPHATE COMPLEX. AUTHORS DID NOT PROVIDE INFORMATION REGARDING THE ORIGIN OF THE PHOSPHATE GROUP. 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)91,45019
Polymers90,2192
Non-polymers1,23117
Water14,124784
1
A: Exopolyphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6929
Polymers45,1091
Non-polymers5838
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exopolyphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,75710
Polymers45,1091
Non-polymers6489
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.992, 83.039, 118.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 801 molecules

#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 784 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 7% PEG 4000, 150 mM (NH4)2SO4, 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: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.6→68 Å / Num. obs: 99085 / % possible obs: 94.6 % / Redundancy: 3.7 % / Rsym value: 0.054 / Net I/σ(I): 5.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 11292 / Rsym value: 0.266 / % possible all: 74.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.2.0005phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QB6

2qb6


Resolution: 1.6→67.42 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.731 / SU ML: 0.055 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20139 4945 5 %RANDOM
Rwork0.17062 ---
obs0.17216 94073 94.4 %-
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: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--1.09 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.6→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6287 0 62 784 7133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226430
X-RAY DIFFRACTIONr_bond_other_d0.0010.025886
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.9778645
X-RAY DIFFRACTIONr_angle_other_deg1.253313765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5385781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49324.935310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.533151239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5791540
X-RAY DIFFRACTIONr_chiral_restr0.0710.2963
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027036
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021242
X-RAY DIFFRACTIONr_nbd_refined0.210.21399
X-RAY DIFFRACTIONr_nbd_other0.1740.25993
X-RAY DIFFRACTIONr_nbtor_refined0.1760.23169
X-RAY DIFFRACTIONr_nbtor_other0.0840.23573
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2577
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9391.55090
X-RAY DIFFRACTIONr_mcbond_other0.1511.51599
X-RAY DIFFRACTIONr_mcangle_it1.03926293
X-RAY DIFFRACTIONr_scbond_it1.82932935
X-RAY DIFFRACTIONr_scangle_it2.6284.52351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 257 -
Rwork0.193 5133 -
obs--70.46 %

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