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- PDB-3q46: Magnesium activated Inorganic pyrophosphatase from Thermococcus t... -

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Basic information

Entry
Database: PDB / ID: 3q46
TitleMagnesium activated Inorganic pyrophosphatase from Thermococcus thioreducens bound to hydrolyzed product at 0.99 Angstrom resolution
ComponentsTt-IPPase
KeywordsHYDROLASE / Inorganic Pyrophosphatase
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
PHOSPHATE ION / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesThermococcus thioreducens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.99 Å
AuthorsHughes, R.C. / Coates, L. / Meehan, E.J. / Ng, J.D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Inorganic pyrophosphatase crystals from Thermococcus thioreducens for X-ray and neutron diffraction.
Authors: Hughes, R.C. / Coates, L. / Blakeley, M.P. / Tomanicek, S.J. / Langan, P. / Kovalevsky, A.Y. / Garcia-Ruiz, J.M. / Ng, J.D.
History
DepositionDec 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Sep 17, 2014Group: Database references
Revision 1.3Sep 13, 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 / pdbx_struct_special_symmetry / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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: Tt-IPPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2898
Polymers20,8231
Non-polymers4667
Water5,314295
1
A: Tt-IPPase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)127,73248
Polymers124,9376
Non-polymers2,79642
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
crystal symmetry operation18_654-x+4/3,-x+y+2/3,-z-1/31
Buried area23850 Å2
ΔGint-405 kcal/mol
Surface area34770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.253, 99.253, 98.557
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-224-

HOH

21A-238-

HOH

31A-243-

HOH

41A-288-

HOH

51A-289-

HOH

61A-320-

HOH

71A-380-

HOH

81A-396-

HOH

91A-414-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Tt-IPPase


Mass: 20822.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus thioreducens (archaea) / Strain: OGL-20 / Gene: Tt-IPPase / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta2 / References: UniProt: H2L2L6*PLUS

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Non-polymers , 5 types, 302 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 298 K / pH: 7.5
Details: Hepes, Isopropanol, Magnesium Chloride, Sodium Pyrophosphate, pH 7.5, counter diffusion, free-interface diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionRedundancy: 2.8 % / Av σ(I) over netI: 11.98 / Number: 523484 / Rmerge(I) obs: 0.066 / Χ2: 1.31 / D res high: 0.95 Å / D res low: 50 Å / Num. obs: 1 / % possible obs: 82
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.055097.410.0520.8423.1
1.622.0599.910.0731.4583.1
1.421.6299.910.0681.7463.1
1.291.4210010.0851.4413.1
1.21.2910010.1081.3233
1.131.210010.1371.293
1.071.1399.310.1961.1652.7
1.021.078210.2680.9551.7
0.981.0237.110.4661.1391.3
0.950.984.310.6742.781
ReflectionResolution: 0.95→50 Å / Num. obs: 94537 / % possible obs: 82 % / Redundancy: 2.8 % / Biso Wilson estimate: 6.2 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.9
Reflection shellResolution: 0.95→0.98 Å / Redundancy: 1 % / Rmerge(I) obs: 0.674 / % possible all: 4.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1 Å21.59 Å
Translation1 Å21.59 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UDE

1ude


Resolution: 0.99→18.76 Å / SU ML: 0.08 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.123 4774 5.05 %
Rwork0.11 --
obs0.111 94537 91.7 %
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 131.91 Å2 / ksol: 0.58 e/Å3
Displacement parametersBiso mean: 13.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.0349 Å2-0 Å2-0 Å2
2--1.0349 Å20 Å2
3----2.2506 Å2
Refinement stepCycle: LAST / Resolution: 0.99→18.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1464 0 25 295 1784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0261810
X-RAY DIFFRACTIONf_angle_d2.1522474
X-RAY DIFFRACTIONf_dihedral_angle_d15.651728
X-RAY DIFFRACTIONf_chiral_restr0.124245
X-RAY DIFFRACTIONf_plane_restr0.015328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.99-1.00130.3857490.33991124X-RAY DIFFRACTION34
1.0013-1.0130.27691020.28561618X-RAY DIFFRACTION51
1.013-1.02540.24431330.24472169X-RAY DIFFRACTION68
1.0254-1.03840.22151330.22152556X-RAY DIFFRACTION79
1.0384-1.0520.19641380.19432796X-RAY DIFFRACTION86
1.052-1.06640.21391460.17252911X-RAY DIFFRACTION89
1.0664-1.08170.15511630.15372989X-RAY DIFFRACTION93
1.0817-1.09780.15881650.13053002X-RAY DIFFRACTION93
1.0978-1.1150.13181650.11353104X-RAY DIFFRACTION95
1.115-1.13320.10521720.09683127X-RAY DIFFRACTION96
1.1332-1.15280.09821570.08513139X-RAY DIFFRACTION97
1.1528-1.17370.10641550.08663162X-RAY DIFFRACTION97
1.1737-1.19630.10421500.08493194X-RAY DIFFRACTION98
1.1963-1.22070.09951650.08613169X-RAY DIFFRACTION97
1.2207-1.24730.11961690.08523176X-RAY DIFFRACTION97
1.2473-1.27630.10191820.08263129X-RAY DIFFRACTION98
1.2763-1.30820.09421810.08023183X-RAY DIFFRACTION98
1.3082-1.34350.11091670.08713218X-RAY DIFFRACTION98
1.3435-1.38310.09931670.08423213X-RAY DIFFRACTION99
1.3831-1.42770.11151580.08693236X-RAY DIFFRACTION99
1.4277-1.47870.1081900.08293218X-RAY DIFFRACTION99
1.4787-1.53790.10391570.08353261X-RAY DIFFRACTION99
1.5379-1.60780.10971840.0863233X-RAY DIFFRACTION99
1.6078-1.69260.10311790.08743239X-RAY DIFFRACTION99
1.6926-1.79850.11341770.09373257X-RAY DIFFRACTION100
1.7985-1.93730.10221880.09373274X-RAY DIFFRACTION100
1.9373-2.1320.10751830.09263274X-RAY DIFFRACTION100
2.132-2.43990.09461650.10013300X-RAY DIFFRACTION100
2.4399-3.07180.14241770.11753310X-RAY DIFFRACTION100
3.0718-18.76040.14661570.15343182X-RAY DIFFRACTION93

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