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- PDB-3r5u: The structure of manganese bound Thermococcus thioreducens Inorga... -

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Basic information

Entry
Database: PDB / ID: 3r5u
TitleThe structure of manganese bound Thermococcus thioreducens Inorganic pyrophosphatase
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
: / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesThermococcus thioreducens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsHughes, R.C. / Coates, L. / Meehan, E.J. / Garcia-Ruiz, J.M. / Ng, J.D.
CitationJournal: To be Published
Title: The structure of manganese bound Thermococcus thioreducens Inorganic pyrophosphatase
Authors: Hughes, R.C. / Coates, L. / Meehan, E.J. / Garcia-Ruiz, J.M. / Ng, J.D.
History
DepositionMar 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Sep 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tt-IPPase
B: Tt-IPPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8724
Polymers41,7622
Non-polymers1102
Water7,548419
1
A: Tt-IPPase
B: Tt-IPPase
hetero molecules

A: Tt-IPPase
B: Tt-IPPase
hetero molecules

A: Tt-IPPase
B: Tt-IPPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,61512
Polymers125,2856
Non-polymers3306
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area16800 Å2
ΔGint-133 kcal/mol
Surface area34870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.514, 114.514, 148.438
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-296-

HOH

21A-313-

HOH

31A-407-

HOH

41A-410-

HOH

51A-428-

HOH

61B-295-

HOH

71B-314-

HOH

81B-315-

HOH

91B-372-

HOH

101B-384-

HOH

111B-415-

HOH

Detailshexamer

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Components

#1: Protein Tt-IPPase


Mass: 20880.885 Da / Num. of mol.: 2
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: H0USY5*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 45.15 %
Crystal growTemperature: 298 K / pH: 7.5
Details: HEPES pH 7.5, Polyethylene glycol 8000, Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, 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: May 15, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 28786 / % possible obs: 99.5 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 11
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.154 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å49.48 Å
Translation2 Å49.48 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: 1TWL

1twl


Resolution: 1.92→29.71 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.18 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 1458 5.06 %
Rwork0.15 --
obs0.152 28786 99.9 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.26 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 17.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.0644 Å20 Å2-0 Å2
2--0.0644 Å20 Å2
3----0.1287 Å2
Refinement stepCycle: LAST / Resolution: 1.92→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2869 0 2 419 3290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083147
X-RAY DIFFRACTIONf_angle_d1.0884310
X-RAY DIFFRACTIONf_dihedral_angle_d13.7191208
X-RAY DIFFRACTIONf_chiral_restr0.08438
X-RAY DIFFRACTIONf_plane_restr0.005565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.98730.20291490.15472669X-RAY DIFFRACTION99
1.9873-2.06690.1951310.14722735X-RAY DIFFRACTION100
2.0669-2.16090.22651460.14342705X-RAY DIFFRACTION100
2.1609-2.27480.21721490.1452695X-RAY DIFFRACTION100
2.2748-2.41720.19831420.14492710X-RAY DIFFRACTION100
2.4172-2.60380.21181510.14832735X-RAY DIFFRACTION100
2.6038-2.86560.19571670.16072704X-RAY DIFFRACTION100
2.8656-3.27980.20991390.1512747X-RAY DIFFRACTION100
3.2798-4.13050.17931560.14312771X-RAY DIFFRACTION100
4.1305-29.71410.16951280.15682857X-RAY DIFFRACTION100

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