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- PDB-1twl: Inorganic pyrophosphatase from Pyrococcus furiosus Pfu-264096-001 -

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Basic information

Entry
Database: PDB / ID: 1twl
TitleInorganic pyrophosphatase from Pyrococcus furiosus Pfu-264096-001
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / inorganic pyrophosphatase / structural genomics / protein structure initiative / PSI / Southeast Collaboratory for Structural Genomics / SECSG
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 speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.201 Å
AuthorsZhou, W. / Tempel, W. / Liu, Z.-J. / Chen, L. / Clancy Kelley, L.-L. / Dillard, B.D. / Hopkins, R.C. / Arendall III, W.B. / Rose, J.P. / Eneh, J.C. ...Zhou, W. / Tempel, W. / Liu, Z.-J. / Chen, L. / Clancy Kelley, L.-L. / Dillard, B.D. / Hopkins, R.C. / Arendall III, W.B. / Rose, J.P. / Eneh, J.C. / Hopkins, R.C. / Jenney Jr., F.E. / Lee, H.S. / Li, T. / Poole II, F.L. / Shah, C. / Sugar, F.J. / Adams, M.W.W. / Richardson, J.S. / Richardson, D.C. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Inorganic pyrophosphatase from Pyrococcus furiosus Pfu-264096-001
Authors: Zhou, W. / Tempel, W. / Liu, Z.-J. / Chen, L. / Clancy Kelley, L.-L. / Dillard, B.D. / Hopkins, R.C. / Arendall III, W.B. / Rose, J.P. / ENEH, J.C. / HOPKINS, R.C. / JENNEY JR., F.E. / LEE, ...Authors: Zhou, W. / Tempel, W. / Liu, Z.-J. / Chen, L. / Clancy Kelley, L.-L. / Dillard, B.D. / Hopkins, R.C. / Arendall III, W.B. / Rose, J.P. / ENEH, J.C. / HOPKINS, R.C. / JENNEY JR., F.E. / LEE, H.S. / LI, T. / POOLE II, F.L. / SHAH, C. / SUGAR, F.J. / ADAMS, M.W.W. / Richardson, J.S. / Richardson, D.C. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics
History
DepositionJul 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)21,8551
Polymers21,8551
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Inorganic pyrophosphatase
x 6


Theoretical massNumber of molelcules
Total (without water)131,1306
Polymers131,1306
Non-polymers00
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 area14890 Å2
ΔGint-93 kcal/mol
Surface area35260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)113.434, 113.434, 73.313
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-208-

HOH

21A-213-

HOH

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Components

#1: Protein Inorganic pyrophosphatase / / Pyrophosphate phospho-hydrolase / PPase


Mass: 21855.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PPA, PF0257 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U438, inorganic diphosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.08 Å3/Da / Density % sol: 40.73 %
Crystal growTemperature: 291 K / pH: 8.6
Details: 1.5M K2HPO4, 0.1M TRIS-HCL, pH 8.6, modified microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 9314 / % possible obs: 100 % / Rmerge(I) obs: 0.082
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.280.381199.7
2.28-2.370.3231100
2.37-2.480.2641100
2.48-2.610.2061100
2.61-2.770.1651100
2.77-2.990.1091100
2.99-3.290.0751100
3.29-3.760.0631100
3.76-4.730.0561100
4.73-300.0521100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefmac_5.2.0003refinement
PDB_EXTRACT1data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UDE

1ude


Resolution: 2.201→29.361 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.223 / SU ML: 0.159 / SU R Cruickshank DPI: 0.286 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.23 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 447 4.8 %RANDOM
Rwork0.1936 ---
all0.197 ---
obs0.19657 9313 99.903 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.024 Å2-0.012 Å20 Å2
2---0.024 Å20 Å2
3---0.036 Å2
Refinement stepCycle: LAST / Resolution: 2.201→29.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 0 35 1405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221417
X-RAY DIFFRACTIONr_bond_other_d0.0020.021298
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.961928
X-RAY DIFFRACTIONr_angle_other_deg0.79533001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51523.22662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96115225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.23158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021557
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02300
X-RAY DIFFRACTIONr_nbd_refined0.1910.2216
X-RAY DIFFRACTIONr_nbd_other0.1760.21233
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2677
X-RAY DIFFRACTIONr_nbtor_other0.0830.2793
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.27
X-RAY DIFFRACTIONr_mcbond_it2.3682892
X-RAY DIFFRACTIONr_mcbond_other0.5752340
X-RAY DIFFRACTIONr_mcangle_it3.43531394
X-RAY DIFFRACTIONr_mcangle_other1.9831172
X-RAY DIFFRACTIONr_scbond_it2.1422624
X-RAY DIFFRACTIONr_scbond_other0.73521230
X-RAY DIFFRACTIONr_scangle_it3.1573534
X-RAY DIFFRACTIONr_scangle_other1.43231829
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.201-2.2580.311360.25765069598.705
2.258-2.320.406290.228618647100
2.32-2.3860.254290.233612641100
2.386-2.4590.33310.226603634100
2.459-2.5390.344240.2573597100
2.539-2.6280.367250.22559584100
2.628-2.7260.34340.232546580100
2.726-2.8360.279320.227505537100
2.836-2.9610.319260.211496522100
2.961-3.1040.267250.194476501100
3.104-3.270.319210.217465486100
3.27-3.4660.409200.189432452100
3.466-3.7010.178220.168411433100
3.701-3.9930.158140.142380394100
3.993-4.3660.189220.137358380100
4.366-4.8680.178210.142310331100
4.868-5.5950.155120.157289301100
5.595-6.7910.276120.199252264100
6.791-9.3570.20990.239198207100
9.357-29.3610.41430.267133136100

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