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- PDB-3d63: Crystal structure of inorganic pyrophosphatase from Burkholderia ... -

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Basic information

Entry
Database: PDB / ID: 3d63
TitleCrystal structure of inorganic pyrophosphatase from Burkholderia pseudomallei
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / structural genomics / SSGCID / pyrophosphatase / Seattle Structural Genomics Center for Infectious Disease
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 speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionMay 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)64,4213
Polymers64,4213
Non-polymers00
Water4,324240
1
A: Inorganic pyrophosphatase

B: Inorganic pyrophosphatase

C: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)64,4213
Polymers64,4213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x+1/2,y+1/2,-z-11
crystal symmetry operation3_555-x+1/2,y+1/2,-z1
Buried area4340 Å2
ΔGint-36.7 kcal/mol
Surface area23780 Å2
MethodPISA
2
A: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)21,4741
Polymers21,4741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)21,4741
Polymers21,4741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)21,4741
Polymers21,4741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.886, 122.019, 71.775
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 5 / Auth seq-ID: 4 - 174 / Label seq-ID: 25 - 195

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein Inorganic pyrophosphatase


Mass: 21473.625 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: N-terminal 6-His tag and 3C protease cleavage. The un-cleaved protein was crystallized.
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: ppa, BURPS1710b_1237 / Plasmid: Ava0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JUV5, inorganic diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES ALA C(-19) TO HIS C(-14) THAT ARE PRESENT IN COORDINATES, ARE THE FRAGMENT OF N-TERMINAL ...RESIDUES ALA C(-19) TO HIS C(-14) THAT ARE PRESENT IN COORDINATES, ARE THE FRAGMENT OF N-TERMINAL EXPRESSION TAG THAT COULD BELONG TO EITHER CHAIN C OR CHAIN B. THE CHAIN ID C HAS BEEN ASSIGNED FOR THIS FRAGMENT BASED ONLY ON ITS PROXIMITY TO THAT CHAIN. THE UNCERTAINITY IN CHAIN ID ASSIGNMENT IS DUE TO ABSENCE OF ELECTRON DENSITY FOR RESIDUE (-13) AND FEW RESIDUES THAT FOLLOW.

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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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 100 mM Potassium phosphate pH 6.7, 49% PEG 200, 12.3 mg/mL Protein, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.2→61.9 Å / Num. obs: 37853 / % possible obs: 99.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 4.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.2-2.325.30.5561.20.556197.9
2.32-2.465.40.3931.90.393199
2.46-2.635.50.3131.50.313199
2.63-2.845.60.2343.10.234199.4
2.84-3.115.80.1614.40.161199.6
3.11-3.486.10.1215.60.1211100
3.48-4.026.50.0947.10.0941100
4.02-4.926.60.0767.50.0761100
4.92-6.966.50.0678.50.0671100
6.96-61.95.70.05890.058199.7

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→61.9 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.863 / SU B: 8.583 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29995 1671 5 %RANDOM
Rwork0.23087 ---
obs0.23432 33242 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.527 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å20 Å2
2---0.61 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.3→61.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4015 0 0 240 4255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224111
X-RAY DIFFRACTIONr_bond_other_d0.0010.022738
X-RAY DIFFRACTIONr_angle_refined_deg1.71.9685589
X-RAY DIFFRACTIONr_angle_other_deg1.48836743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7435520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90725.233172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.23515671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6971512
X-RAY DIFFRACTIONr_chiral_restr0.0860.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214569
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02765
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.711.52610
X-RAY DIFFRACTIONr_mcbond_other0.1551.51050
X-RAY DIFFRACTIONr_mcangle_it1.30724212
X-RAY DIFFRACTIONr_scbond_it1.73631501
X-RAY DIFFRACTIONr_scangle_it2.8364.51377
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A993MEDIUM POSITIONAL0.380.5
B993MEDIUM POSITIONAL0.30.5
C993MEDIUM POSITIONAL0.510.5
A1172LOOSE POSITIONAL0.615
B1172LOOSE POSITIONAL0.615
C1172LOOSE POSITIONAL0.865
A993MEDIUM THERMAL0.422
B993MEDIUM THERMAL0.642
C993MEDIUM THERMAL0.712
A1172LOOSE THERMAL0.5410
B1172LOOSE THERMAL0.6510
C1172LOOSE THERMAL0.7110
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 102 -
Rwork0.274 2291 -
obs--98.48 %

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