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- PDB-3r5v: The structure of calcium bound Thermococcus thioreducens inorgani... -

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Basic information

Entry
Database: PDB / ID: 3r5v
TitleThe structure of calcium bound Thermococcus thioreducens inorganic pyrophosphatase at 298K
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 / FIXED MODEL / Resolution: 1.65 Å
AuthorsHughes, R.C. / Meehan, E.J. / Coates, L. / Ng, J.D.
CitationJournal: To be Published
Title: The structure of calcium bound Thermococcus thioreducens inorganic pyrophosphatase at 298K
Authors: Hughes, R.C. / Meehan, E.J. / Coates, L. / Ng, J.D.
History
DepositionMar 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Structure summary
Category: audit_author / pdbx_distant_solvent_atoms ...audit_author / pdbx_distant_solvent_atoms / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / software / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _audit_author.name / _software.name / _struct_conf.pdbx_PDB_helix_id
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_alt_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_alt_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.pdbx_ptnr1_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
C: Tt-IPPase
D: Tt-IPPase
E: Tt-IPPase
F: Tt-IPPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,88015
Polymers125,2856
Non-polymers5959
Water11,025612
1
A: Tt-IPPase
C: Tt-IPPase
E: Tt-IPPase
hetero molecules

A: Tt-IPPase
C: Tt-IPPase
E: Tt-IPPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,99816
Polymers125,2856
Non-polymers71310
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area17230 Å2
ΔGint-191 kcal/mol
Surface area35450 Å2
MethodPISA
2
B: Tt-IPPase
D: Tt-IPPase
F: Tt-IPPase
hetero molecules

B: Tt-IPPase
D: Tt-IPPase
F: Tt-IPPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,76214
Polymers125,2856
Non-polymers4778
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area17150 Å2
ΔGint-190 kcal/mol
Surface area35800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.092, 95.564, 113.769
Angle α, β, γ (deg.)90.00, 98.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-368-

HOH

21B-385-

HOH

Detailshexamer

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Components

#1: Protein
Tt-IPPase


Mass: 20880.885 Da / Num. of mol.: 6
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 298 K / Method: counter diffusion, free-interface diffusion / pH: 6.5
Details: Hepes, MPD, Na acetate, Calcium Chloride, pH 6.5, counter diffusion, free-interface diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 127937 / % possible obs: 83.8 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.055 / Χ2: 1.352 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.681.40.3992591.026169.1
1.68-1.711.50.363100100.963175.1
1.71-1.741.60.321104691.02178.5
1.74-1.781.60.27109321.081182.1
1.78-1.821.70.217109331.11183.1
1.82-1.861.70.187111751.07183.6
1.86-1.91.70.155112271.127184
1.9-1.961.70.124111731.133184.1
1.96-2.011.70.111111581.233183.9
2.01-2.081.70.097111801.21183.9
2.08-2.151.70.083112471.427184.1
2.15-2.241.80.073112011.392184.3
2.24-2.341.80.062111991.352184.3
2.34-2.461.80.055112461.391184.1
2.46-2.621.70.051112161.504184.7
2.62-2.821.70.051113111.752184.7
2.82-3.111.70.047113921.606185.3
3.11-3.551.70.043117131.564187.8
3.55-4.481.80.043122911.591192.5
4.48-501.90.046129431.732197.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: FIXED MODEL
Starting model: 3I98

3i98


Resolution: 1.65→46.235 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.17 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1633 6084 5.01 %
Rwork0.1216 --
obs0.1237 121472 90.08 %
all-132456 -
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.023 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso max: 524.61 Å2 / Biso mean: 25.7749 Å2 / Biso min: 8.09 Å2
Baniso -1Baniso -2Baniso -3
1--1.3238 Å20 Å21.1477 Å2
2--1.5842 Å20 Å2
3----0.2603 Å2
Refinement stepCycle: LAST / Resolution: 1.65→46.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8620 0 30 612 9262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069617
X-RAY DIFFRACTIONf_angle_d1.04813182
X-RAY DIFFRACTIONf_chiral_restr0.0711319
X-RAY DIFFRACTIONf_plane_restr0.0051739
X-RAY DIFFRACTIONf_dihedral_angle_d13.8433722
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.7090.29715440.202197701031477
1.709-1.77740.20885280.1416105351106382
1.7774-1.85830.18835860.1127109351152186
1.8583-1.95630.17365870.1093113561194389
1.9563-2.07880.16866450.1094115881223391
2.0788-2.23930.15676400.104118461248693
2.2393-2.46470.16376160.1079120831269994
2.4647-2.82130.15566370.1204121531279095
2.8213-3.55430.16526200.1286123391295996
3.5543-46.25280.14076810.1244127831346499

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