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- PDB-5c5v: Recombinant Inorganic Pyrophosphatase from T brucei brucei -

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Basic information

Entry
Database: PDB / ID: 5c5v
TitleRecombinant Inorganic Pyrophosphatase from T brucei brucei
ComponentsAcidocalcisomal pyrophosphatase
KeywordsHYDROLASE / EF-hand / PPase domain / Ca binding protein
Function / homology
Function and homology information


pyrophosphatase activity / inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / post-transcriptional regulation of gene expression / magnesium ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
Inorganic Pyrophosphatase / Inorganic pyrophosphatase / Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / EF-hand domain pair / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
IMIDODIPHOSPHORIC ACID / BROMIDE ION / Inorganic diphosphatase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsJamwal, A. / Yogavel, M. / Sharma, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology,Government of India India
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural and Functional Highlights of Vacuolar Soluble Protein 1 from Pathogen Trypanosoma brucei brucei
Authors: Jamwal, A. / Round, A.R. / Bannwarth, L. / Venien-Bryan, C. / Belrhali, H. / Yogavel, M. / Sharma, A.
History
DepositionJun 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acidocalcisomal pyrophosphatase
B: Acidocalcisomal pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,51620
Polymers79,6132
Non-polymers90318
Water3,567198
1
A: Acidocalcisomal pyrophosphatase
B: Acidocalcisomal pyrophosphatase
hetero molecules

A: Acidocalcisomal pyrophosphatase
B: Acidocalcisomal pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,03340
Polymers159,2274
Non-polymers1,80636
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_685-x+1,-y+3,z1
Buried area19840 Å2
ΔGint-343 kcal/mol
Surface area54120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.210, 104.210, 215.513
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain B and segidB0

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acidocalcisomal pyrophosphatase


Mass: 39806.672 Da / Num. of mol.: 2 / Fragment: UNP residues 73-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb11.02.4910 / Production host: Escherichia coli (E. coli) / References: UniProt: Q384W5

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Non-polymers , 6 types, 216 molecules

#2: Chemical ChemComp-2PN / IMIDODIPHOSPHORIC ACID


Mass: 176.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H5NO6P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 3.67 Å3/Da / Density % sol: 66.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Single Cuboid shaped crystal 9 % PEG 8000, 18 % ethylene glycol, 0.02 M halide, 0.1 M bicine/trizma pH 8.0 and 0. 1 M spermine tetrahydrochloride
PH range: 8.0-8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 50422 / % possible obs: 99.9 % / Redundancy: 10.9 % / Biso Wilson estimate: 56.71 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.022 / Rrim(I) all: 0.074 / Χ2: 0.942 / Net I/av σ(I): 32.065 / Net I/σ(I): 9.6 / Num. measured all: 547845
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.39110.65824730.9130.2030.690.632100
2.39-2.43110.51524850.9390.1590.540.628100
2.43-2.48110.51224860.9440.1590.5370.644100
2.48-2.5311.10.4424660.9590.1350.4620.656100
2.53-2.59110.3424690.9730.1040.3560.684100
2.59-2.65110.28724900.9850.0880.30.68100
2.65-2.7111.10.26124760.9850.080.2740.697100
2.71-2.7911.10.20324900.9880.0620.2130.729100
2.79-2.8711.10.16925020.9930.0510.1770.785100
2.87-2.9611.10.13124870.9960.040.1380.855100
2.96-3.0711.10.11525200.9960.0350.1210.892100
3.07-3.1911.10.09724980.9970.030.1020.981100
3.19-3.3311.10.07925070.9980.0240.0821.116100
3.33-3.51110.07225140.9990.0220.0761.347100
3.51-3.73110.06925370.9980.0210.0721.297100
3.73-4.0210.80.0725420.9980.0210.0731.354100
4.02-4.4210.40.07125460.9980.0230.0751.249100
4.42-5.0610.20.06925720.9970.0220.0731.2299.9
5.06-6.3710.60.05326170.9980.0170.0561.243100
6.37-509.80.03527450.9990.0110.0371.15298

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→39.83 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 1964 3.97 %
Rwork0.199 47507 -
obs0.2006 49471 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.65 Å2 / Biso mean: 64.4024 Å2 / Biso min: 18.29 Å2
Refinement stepCycle: final / Resolution: 2.35→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5529 0 45 200 5774
Biso mean--55.6 61.23 -
Num. residues----684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075710
X-RAY DIFFRACTIONf_angle_d1.0617725
X-RAY DIFFRACTIONf_chiral_restr0.044797
X-RAY DIFFRACTIONf_plane_restr0.005984
X-RAY DIFFRACTIONf_dihedral_angle_d12.5732092
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3307X-RAY DIFFRACTION7.301TORSIONAL
12B3307X-RAY DIFFRACTION7.301TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3479-2.40660.33081300.28433180331094
2.4066-2.47160.27151340.25983245337995
2.4716-2.54440.28921340.25983285341996
2.5444-2.62650.28851380.24813283342197
2.6265-2.72030.30141360.25833330346698
2.7203-2.82920.3221390.25523354349398
2.8292-2.95790.22991410.24083363350499
2.9579-3.11380.31431410.23873404354599
3.1138-3.30880.25771420.244734263568100
3.3088-3.56420.261430.21234363579100
3.5642-3.92260.21361420.189634663608100
3.9226-4.48950.21461440.169434883632100
4.4895-5.65370.20591470.163435453692100
5.6537-39.83580.21871530.17423702385599
Refinement TLS params.Method: refined / Origin x: 48.4145 Å / Origin y: 166.0983 Å / Origin z: 48.7385 Å
111213212223313233
T0.2833 Å2-0.0445 Å20.0122 Å2-0.4601 Å2-0.0241 Å2--0.4717 Å2
L0.4441 °20.022 °20.0068 °2-0.5217 °2-0.0278 °2--1.1863 °2
S0.0806 Å °-0.0894 Å °-0.0192 Å °0.0283 Å °-0.1211 Å °-0.008 Å °-0.0141 Å °0.0356 Å °0.0354 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA73 - 414
2X-RAY DIFFRACTION1allB73 - 414
3X-RAY DIFFRACTION1allC415 - 416
4X-RAY DIFFRACTION1allD417 - 424
5X-RAY DIFFRACTION1allE7 - 427
6X-RAY DIFFRACTION1allF3 - 6
7X-RAY DIFFRACTION1allF7
8X-RAY DIFFRACTION1allF10
9X-RAY DIFFRACTION1allF11
10X-RAY DIFFRACTION1allG3
11X-RAY DIFFRACTION1allH1

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