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- PDB-3d53: 2.2 A crystal structure of inorganic pyrophosphatase from Rickett... -

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Basic information

Entry
Database: PDB / ID: 3d53
Title2.2 A crystal structure of inorganic pyrophosphatase from Rickettsia prowazekii
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / RICKETTSIA / INORGANIC / PYROPHOSPHATASE / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID / Magnesium / Metal-binding
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 speciesRickettsia prowazekii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: 2.2 A crystal structure of inorganic pyrophosphatase from Rickettsia prowazekii.
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMay 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase
D: Inorganic pyrophosphatase
E: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,76429
Polymers117,7796
Non-polymers98523
Water9,854547
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-103.4 kcal/mol
Surface area42530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.970, 115.230, 139.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 19629.762 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia prowazekii (bacteria) / Strain: Madrid E / Gene: ppa, RP589 / Plasmid: pET28-SMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZCW5, inorganic diphosphatase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cl
#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.: 547 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 2.5M NaCl, 0.1M Na acetate pH 4.5, 0.2M Li2SO4, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 25, 2008 / Details: Adjustable focusing mirrors
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionResolution: 2.2→34.94 Å / Num. obs: 56518 / % possible obs: 98.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.325.90.5241.54690780160.52497.6
2.32-2.465.90.4491.74514576630.44998.1
2.46-2.635.90.3462.24285172210.34698.6
2.63-2.8460.25334057667510.25398.6
2.84-3.116.10.1634.53853162700.16398.9
3.11-3.486.40.11563696957500.11599.8
3.48-4.026.80.0827.63474350980.08299.9
4.02-4.926.90.0648.93002143630.064100
4.92-6.966.80.0669.12319934280.06699.9
6.96-34.945.80.0529.91130219580.05298.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å34.06 Å
Translation2.8 Å34.06 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2EIP

2eip


Resolution: 2.2→33.56 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.013 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2855 5.1 %RANDOM
Rwork0.217 ---
obs0.22 56507 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.576 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8072 0 38 547 8657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228330
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.97211254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90151038
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98625.506356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.913151591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9161524
X-RAY DIFFRACTIONr_chiral_restr0.0910.21268
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026102
X-RAY DIFFRACTIONr_nbd_refined0.1910.23775
X-RAY DIFFRACTIONr_nbtor_refined0.3020.25641
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2535
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.211
X-RAY DIFFRACTIONr_mcbond_it0.6011.55270
X-RAY DIFFRACTIONr_mcangle_it1.04528336
X-RAY DIFFRACTIONr_scbond_it1.4433449
X-RAY DIFFRACTIONr_scangle_it2.3024.52904
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 207 -
Rwork0.254 3825 -
all-4032 -
obs--96.6 %

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