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- PDB-1sxv: 1.3A Crystal structure of rv3628, Mycobacterium tuberculosis inor... -

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Basic information

Entry
Database: PDB / ID: 1sxv
Title1.3A Crystal structure of rv3628, Mycobacterium tuberculosis inorganic pyrophosphatase (PPase) at pH5.0
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / Mycobacterium tuberculosis / structural genomics / inorganic pyrophosphatase / PPase
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / host cell surface / magnesium ion binding / extracellular region / plasma membrane / cytosol
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 / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBenini, S. / Wilson, K.S.
CitationJournal: To be Published
Title: Mycobacterium tuberculosis Rv3628, yet another inorganic pyrophosphatase or a possible drug target?
Authors: Benini, S. / Wilson, K.S.
History
DepositionMar 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9165
Polymers19,5441
Non-polymers3724
Water4,288238
1
A: Inorganic pyrophosphatase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)119,49830
Polymers117,2646
Non-polymers2,23424
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
crystal symmetry operation10_775-y+2,-x+2,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_575x,x-y+2,-z+1/21
Buried area18100 Å2
ΔGint-171 kcal/mol
Surface area36480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)98.460, 98.460, 97.353
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-340-

HOH

21A-512-

HOH

31A-518-

HOH

41A-535-

HOH

51A-538-

HOH

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Components

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


Mass: 19543.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: PPA, RV3628, MT3730, MTCY15C10.24, MB3652 / Plasmid: modified pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P65746, UniProt: P9WI55*PLUS, inorganic diphosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 3.49 Å3/Da / Density % sol: 64.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.7 M ammonium sulphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 6, 2004 / Details: mirrors
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.3→84.5 Å / Num. all: 68651 / Num. obs: 68086 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 32
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 3.15 / Num. unique all: 3296 / Rsym value: 0.683 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PRD

2prd


Resolution: 1.3→84.5 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.482 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.037 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16945 3444 5.1 %RANDOM
Rwork0.15437 ---
all0.15514 64618 --
obs0.15514 64618 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.899 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.32 Å20 Å2
2--0.63 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.3→84.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1276 0 23 238 1537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221420
X-RAY DIFFRACTIONr_bond_other_d0.0030.021273
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9641929
X-RAY DIFFRACTIONr_angle_other_deg1.07732987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3035164
X-RAY DIFFRACTIONr_chiral_restr0.0970.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021560
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02294
X-RAY DIFFRACTIONr_nbd_refined0.2250.2250
X-RAY DIFFRACTIONr_nbd_other0.260.21507
X-RAY DIFFRACTIONr_nbtor_other0.0880.2835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2163
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0650.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3330.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.222
X-RAY DIFFRACTIONr_mcbond_it1.3961.5824
X-RAY DIFFRACTIONr_mcangle_it2.04321353
X-RAY DIFFRACTIONr_scbond_it2.6873596
X-RAY DIFFRACTIONr_scangle_it3.9154.5573
X-RAY DIFFRACTIONr_rigid_bond_restr0.81111420
X-RAY DIFFRACTIONr_sphericity_free10.5355238
X-RAY DIFFRACTIONr_sphericity_bonded5.34351381
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.209 239
Rwork0.208 4632

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