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- PDB-1wpp: Structure of Streptococcus gordonii inorganic pyrophosphatase -

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Basic information

Entry
Database: PDB / ID: 1wpp
TitleStructure of Streptococcus gordonii inorganic pyrophosphatase
ComponentsProbable manganese-dependent inorganic pyrophosphatase
KeywordsHYDROLASE / inorganic pyrophosphatase / metal binding / inhibition
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / manganese ion binding / cytoplasm
Similarity search - Function
Manganese-dependent inorganic pyrophosphatase, probable / DHHA2 domain / DHHA2 domain / DHHA2 domain superfamily / DHHA2 domain / DHHA2 / inorganic pyrophosphatase (n-terminal core) / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family ...Manganese-dependent inorganic pyrophosphatase, probable / 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
Probable manganese-dependent inorganic pyrophosphatase
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsFabrichniy, I.P. / Lehtio, L. / Salminen, A. / Baykov, A.A. / Lahti, R. / Goldman, A.
CitationJournal: Biochemistry / Year: 2004
Title: Structural Studies of Metal Ions in Family II Pyrophosphatases: The Requirement for a Janus Ion
Authors: Fabrichniy, I.P. / Lehtio, L. / Salminen, A. / Zyryanov, A.B. / Baykov, A.A. / Lahti, R. / Goldman, A.
History
DepositionSep 9, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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.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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable manganese-dependent inorganic pyrophosphatase
B: Probable manganese-dependent inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,97313
Polymers67,0992
Non-polymers87311
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-274 kcal/mol
Surface area24650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.080, 148.960, 43.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-1034-

HOH

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Components

#1: Protein Probable manganese-dependent inorganic pyrophosphatase / Pyrophosphate phospho-hydrolase / PPase


Mass: 33549.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Strain: str. Challis / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P95765, inorganic diphosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / 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: 2.3 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, streak seeding / pH: 5.6
Details: sodium citrate, ammonium sulphate, K/Na-tartrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, STREAK SEEDING, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.879 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 8, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.879 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 40182 / Num. obs: 40182 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.05→2.1 Å / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→19.69 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.258 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21647 2010 5 %RANDOM
Rwork0.16658 ---
all0.16912 38171 --
obs0.16912 38171 100 %-
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: 22.56 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å20 Å2
2---1.35 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4704 0 35 536 5275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0214886
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.966635
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8895632
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_restr0.1110.2773
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023712
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.180.12238
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.1811
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.52
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.155
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.138
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8551.53126
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49425029
X-RAY DIFFRACTIONr_scbond_it2.54431760
X-RAY DIFFRACTIONr_scangle_it4.0934.51606
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.278 147
Rwork0.189 2777

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