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- PDB-3gvf: 1.7 Angstrom crystal structure of inorganic pyrophosphatase from ... -

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Basic information

Entry
Database: PDB / ID: 3gvf
Title1.7 Angstrom crystal structure of inorganic pyrophosphatase from burkholderia pseudomallei bound with phosphate
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / structural genomics / inorganic pyrophosphatase / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesBurkholderia pseudomallei 1710b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
DepositionMar 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Sep 6, 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_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0377
Polymers21,4741
Non-polymers5646
Water2,396133
1
A: Inorganic pyrophosphatase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)132,22342
Polymers128,8426
Non-polymers3,38136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/21
crystal symmetry operation11_455-x+y-1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area18310 Å2
ΔGint-177 kcal/mol
Surface area38390 Å2
MethodPISA
2
A: Inorganic pyrophosphatase
hetero molecules

A: Inorganic pyrophosphatase
hetero molecules

A: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,11121
Polymers64,4213
Non-polymers1,69118
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area6810 Å2
ΔGint-77 kcal/mol
Surface area21530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.212, 100.212, 110.667
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-177-

K

21A-290-

HOH

DetailsUNKNOWN

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Inorganic pyrophosphatase


Mass: 21473.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei 1710b (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

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Non-polymers , 6 types, 139 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.74 Å3/Da / Density % sol: 67.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 100 MM NA/K PHOSPHATE, 50% PEG 200, PH 6.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Aug 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 33131 / % possible obs: 98.2 % / Redundancy: 14 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.2
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.632 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EIY

3eiy


Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.792 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1689 5.1 %RANDOM
Rwork0.175 ---
obs0.175 33036 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.27 Å20 Å2
2--0.55 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1325 0 34 133 1492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221384
X-RAY DIFFRACTIONr_bond_other_d0.0010.02933
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9881873
X-RAY DIFFRACTIONr_angle_other_deg0.80432295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2225173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.19825.35756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37915218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.205154
X-RAY DIFFRACTIONr_chiral_restr0.070.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211513
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02253
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_it0.4461.5867
X-RAY DIFFRACTIONr_mcbond_other0.1051.5349
X-RAY DIFFRACTIONr_mcangle_it0.87221399
X-RAY DIFFRACTIONr_scbond_it1.5563517
X-RAY DIFFRACTIONr_scangle_it2.5954.5474
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 116 -
Rwork0.182 2290 -
obs--98.24 %
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)
13.28810.02960.60164.8555-2.68263.26940.11370.3606-0.0751-0.4451-0.03120.16530.3766-0.0327-0.08250.20830.0025-0.01770.12550.05990.0774-48.777-11.4781.409
21.5585-0.42570.99331.5118-1.56522.97220.05210.0721-0.0344-0.1556-0.0318-0.04140.09520.1836-0.02030.14970.0118-0.00050.07580.01010.0524-42.617-21.1515.495
34.73530.7348-0.22314.0618-1.166618.2033-0.06640.4887-0.0373-0.8768-0.0598-0.37210.19120.21070.12620.29070.03860.03710.12250.00070.0746-39.718-26.3615.007
411.41681.81558.11673.76912.031614.1493-0.23120.43680.158-0.28050.1439-0.1618-0.72310.27160.08720.15880.05070.05370.10050.00950.0552-37.929-27.8749.267
53.2899-0.88411.34281.90470.17541.3191-0.02510.06570.1005-0.14130.0371-0.2657-0.1290.169-0.01210.1007-0.00620.0150.08920.01330.0653-36.958-20.83420.439
63.78821.2538-3.78188.0311-4.067412.21480.16820.1333-0.1261-0.3994-0.2835-0.51630.4390.8250.11520.17720.07340.02760.18650.03860.0804-37.876-14.1172.617
71.3350.36220.09872.0957-0.76131.21110.03640.05880.1040.06420.01220.0711-0.06790.0252-0.04860.1510.0010.00150.06050.02320.0467-47.914-13.08213.877
816.9433-12.6315-0.16149.911-1.20495.39860.66071.18180.3567-0.9872-1.1025-0.57360.8630.90360.44180.65580.07390.2980.42960.20610.4922-28.894-9.47811.68
94.61820.7568-0.3423.1950.11462.52970.1196-0.01460.44780.1919-0.04530.2009-0.1725-0.0769-0.07430.18340.00270.00520.05860.03840.0827-50.616-7.08115.283
106.4241-4.3240.99744.8442-0.63971.6245-0.1193-0.03960.26260.1070.0082-0.2526-0.29910.10220.11110.1519-0.055-0.0010.06690.02040.0762-37.292-8.51522.749
115.0362-7.92663.122817.1138-7.08963.24510.15010.22980.6928-0.8074-0.6712-1.54030.22790.52430.52120.1964-0.06010.08740.26630.02250.3103-27.385-11.53416.946
123.9735-1.8486-2.574910.46397.903412.0130.11080.33880.1856-0.4351-0.1051-0.2292-0.28270.3621-0.00570.14590.0150.01650.13950.10090.0925-39.13-4.7941.039
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 16
2X-RAY DIFFRACTION2A17 - 30
3X-RAY DIFFRACTION3A31 - 37
4X-RAY DIFFRACTION4A38 - 44
5X-RAY DIFFRACTION5A45 - 56
6X-RAY DIFFRACTION6A57 - 69
7X-RAY DIFFRACTION7A70 - 92
8X-RAY DIFFRACTION8A93 - 103
9X-RAY DIFFRACTION9A104 - 120
10X-RAY DIFFRACTION10A121 - 144
11X-RAY DIFFRACTION11A145 - 158
12X-RAY DIFFRACTION12A159 - 175

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