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- PDB-3sw5: Crystal structure of inorganic pyrophosphatase from Bartonella he... -

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Basic information

Entry
Database: PDB / ID: 3sw5
TitleCrystal structure of inorganic pyrophosphatase from Bartonella henselae
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / SSGCID / 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
(2S)-2-hydroxybutanedioic acid / Inorganic pyrophosphatase / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of inorganic pyrophosphatase from Bartonella henselae
Authors: SSGCID / Gardberg, A. / Clifton, M.C. / Staker, B. / Stewart, L.
History
DepositionJul 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Sep 13, 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)122,91212
Polymers122,1086
Non-polymers8056
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16600 Å2
ΔGint-101 kcal/mol
Surface area38010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.860, 68.960, 74.480
Angle α, β, γ (deg.)90.37, 113.38, 119.79
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 6 / Auth seq-ID: 1 - 200 / Label seq-ID: 1 - 200

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

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


Mass: 20351.250 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Gene: ppa, BH01690 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6G4Y0, UniProt: A0A0H3M4F9*PLUS, inorganic diphosphatase
#2: Chemical
ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid


Mass: 134.087 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9.79
Details: Internal tracking number 223591H12. Focus screen based on PACT D6. 100 mM MMT Buffer pH 9.79, 27.04 (%w/v) Polyethylene glycol 1500 BaheA00347aA1_PS00395 at 66.9 mg/ml., VAPOR DIFFUSION, ...Details: Internal tracking number 223591H12. Focus screen based on PACT D6. 100 mM MMT Buffer pH 9.79, 27.04 (%w/v) Polyethylene glycol 1500 BaheA00347aA1_PS00395 at 66.9 mg/ml., VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03317 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2011
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 68367 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 36.44 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.0530.4042.614974501695.2
2.05-2.110.2973.714277483693.4
2.11-2.170.2354.314440483395.6
2.17-2.240.201513748461795.3
2.24-2.310.1526.913010441992.8
2.31-2.390.1337.213061438796.1
2.39-2.480.1118.612563421996.7
2.48-2.580.0959.912053404496.3
2.58-2.70.08810.911575390096.2
2.7-2.830.0711311173377496.6
2.83-2.980.05516.210656362596.9
2.98-3.160.04818.39817335096.6
3.16-3.380.04121.39240317496.7
3.38-3.650.03724.38475294395.6
3.65-40.03426.47663266295.8
4-4.470.0328.47054242996
4.47-5.160.0329.36291216796.6
5.16-6.320.03128.65428187897.2
6.32-8.940.03229.74018139796.7
8.94-500.03330188569785.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å50.43 Å
Translation2.5 Å50.43 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementMethod to determine structure: molecular replacement
Starting model: PDB entry 3FQ3

3fq3


Resolution: 2→36.63 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.512 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3442 5 %RANDOM
Rwork0.185 ---
obs0.187 68364 95.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.502 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20.2 Å21.38 Å2
2---0.42 Å20.21 Å2
3---2.09 Å2
Refinement stepCycle: LAST / Resolution: 2→36.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7936 0 54 296 8286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228255
X-RAY DIFFRACTIONr_bond_other_d0.0010.025365
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.97211298
X-RAY DIFFRACTIONr_angle_other_deg0.886313194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79351051
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.92224.89364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48151239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.011530
X-RAY DIFFRACTIONr_chiral_restr0.0830.21256
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219317
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021573
X-RAY DIFFRACTIONr_mcbond_it0.7711.55195
X-RAY DIFFRACTIONr_mcbond_other0.1861.52072
X-RAY DIFFRACTIONr_mcangle_it1.42928398
X-RAY DIFFRACTIONr_scbond_it2.23833060
X-RAY DIFFRACTIONr_scangle_it3.5984.52888
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2103 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ALOOSE POSITIONAL0.235
BLOOSE POSITIONAL0.25
CLOOSE POSITIONAL0.255
DLOOSE POSITIONAL0.215
ELOOSE POSITIONAL0.275
FLOOSE POSITIONAL0.235
ALOOSE THERMAL2.2910
BLOOSE THERMAL1.4910
CLOOSE THERMAL1.4910
DLOOSE THERMAL1.5810
ELOOSE THERMAL2.0310
FLOOSE THERMAL1.6110
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 246 -
Rwork0.261 4759 -
all-5005 -
obs--95.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1061-0.01050.03861.37970.20670.7321-0.0235-0.11080.17010.0706-0.00830.0604-0.0177-0.07340.03180.04570.02810.00790.0435-0.04560.115-14.33839.475-21.736
21.8658-0.0711-0.17741.040.5771.06220.04420.3863-0.1205-0.0519-0.14630.2123-0.0791-0.17230.10210.01770.0058-0.00860.1745-0.09790.1082-22.06118.406-46.79
31.5503-0.41590.01380.9726-0.38620.8895-0.0071-0.18270.26790.0599-0.0093-0.1666-0.06970.05660.01640.0140.0011-0.01220.0755-0.05480.131317.41529.693-22.916
40.9342-0.2714-0.44181.0399-0.01561.48720.01010.1176-0.1544-0.1548-0.09190.00060.1361-0.04440.08180.05570.02850.01960.0636-0.04190.08419.4387.653-47.846
51.302-0.18640.44050.8768-0.00911.24070.0420.35740.3138-0.1619-0.0848-0.1642-0.06720.09170.04290.10440.04550.0550.11240.0880.15052.64639.953-51.372
61.3938-0.2064-0.360.83430.32130.9646-0.0993-0.1775-0.28910.16290.0150.08320.13460.02090.08420.0783-0.00940.05470.0470.03530.1339-6.8737.45-17.907
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 174
2X-RAY DIFFRACTION2B3 - 174
3X-RAY DIFFRACTION3C3 - 174
4X-RAY DIFFRACTION4D3 - 174
5X-RAY DIFFRACTION5E3 - 174
6X-RAY DIFFRACTION6F3 - 174

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