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- PDB-1qez: SULFOLOBUS ACIDOCALDARIUS INORGANIC PYROPHOSPHATASE: AN ARCHAEL P... -

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Basic information

Entry
Database: PDB / ID: 1qez
TitleSULFOLOBUS ACIDOCALDARIUS INORGANIC PYROPHOSPHATASE: AN ARCHAEL PYROPHOSPHATASE.
ComponentsPROTEIN (INORGANIC PYROPHOSPHATASE)
KeywordsHYDROLASE / INORGANIC PYROPHOSPHATASE / THERMOSTABILITY / MAGNESIUM
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Inorganic Pyrophosphatase / Inorganic pyrophosphatase / Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Inorganic pyrophosphatase
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLeppanen, V.-M. / Nummelin, H. / Hansen, T. / Lahti, R. / Schafer, G. / Goldman, A.
CitationJournal: Protein Sci. / Year: 1999
Title: Sulfolobus acidocaldarius inorganic pyrophosphatase: structure, thermostability, and effect of metal ion in an archael pyrophosphatase.
Authors: Leppanen, V.M. / Nummelin, H. / Hansen, T. / Lahti, R. / Schafer, G. / Goldman, A.
History
DepositionApr 6, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 14, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 16, 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_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_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_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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (INORGANIC PYROPHOSPHATASE)
B: PROTEIN (INORGANIC PYROPHOSPHATASE)
C: PROTEIN (INORGANIC PYROPHOSPHATASE)
D: PROTEIN (INORGANIC PYROPHOSPHATASE)
E: PROTEIN (INORGANIC PYROPHOSPHATASE)
F: PROTEIN (INORGANIC PYROPHOSPHATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,56412
Polymers116,4186
Non-polymers1466
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13180 Å2
ΔGint-127 kcal/mol
Surface area38630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.120, 98.730, 107.250
Angle α, β, γ (deg.)90.00, 78.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.4949, 0.4912, -0.7168), (-0.2223, 0.7259, 0.6509), (0.8401, 0.4814, -0.25)3.4738, -19.2814, 41.0586
2given(-0.4731, -0.2392, 0.8479), (0.4933, 0.7255, 0.4799), (-0.73, 0.6453, -0.2253)40.5894, -11.8397, 16.1898
3given(0.9138, -0.0185, -0.4058), (-0.0197, -0.9998, 0.0012), (-0.4058, 0.0069, -0.9139)11.1073, 0.0738, 52.3605
4given(-0.1697, -0.4885, 0.8559), (-0.4785, -0.7184, -0.5049), (0.8615, -0.4953, -0.1118)-2.0342, 19.4783, 13.4203
5given(-0.7715, 0.2529, -0.5838), (0.2465, -0.7272, -0.6407), (-0.5865, -0.6382, 0.4987)41.7546, 11.2839, 21.1301

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Components

#1: Protein
PROTEIN (INORGANIC PYROPHOSPHATASE) / PPASE / S-PPASE


Mass: 19402.945 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Cellular location: CYTOPLASM / Plasmid: PET-3A / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P50308, inorganic diphosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.12 Å3/Da / Density % sol: 60.54 %
Crystal growpH: 8 / Details: 4% PEG-8000, 0.2M MGCL2, 0.1M TRIS/HCL PH8.0
Crystal grow
*PLUS
Temperature: 26 ℃ / Method: vapor diffusion / Details: protein solution is mixed 2:1 with well solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
121-26 mg/mlprotein1drop
23.5-4.5 %PEG80001reservoir
30.2 M1reservoirMgCl2
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 38004 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 51 Å2 / Rsym value: 0.091 / Net I/σ(I): 10.1
Reflection shellResolution: 2.7→2.75 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.28 / % possible all: 62.2
Reflection
*PLUS
Num. measured all: 256303 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 62.2 % / Rmerge(I) obs: 0.28

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PRD

2prd


Resolution: 2.7→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 157938.29 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3485 10 %RANDOM
Rwork0.197 ---
obs-34928 92.2 %-
Displacement parametersBiso mean: 38.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7947 0 6 75 8028
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.62
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.7→2.79 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.357 261 10.7 %
Rwork0.319 2171 -
obs--64.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAMETER.ELEMENTSTOPH11.WAT
X-RAY DIFFRACTION3TOPOLOGY.ELEMENTS
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.62

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