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- PDB-2d1g: Structure of Francisella tularensis Acid Phosphatase A (AcpA) bou... -

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Basic information

Entry
Database: PDB / ID: 2d1g
TitleStructure of Francisella tularensis Acid Phosphatase A (AcpA) bound to orthovanadate
Componentsacid phosphatase
KeywordsHYDROLASE / Francisella tularensis / Acid Phosphatase / AcpA / decavanadate / vanadate
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds
Similarity search - Function
Phosphoesterase / Phosphoesterase family / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DECAVANADATE / Chem-ETE / 2-ETHOXYETHANOL / TRIETHYLENE GLYCOL / VANADATE ION / Acid phosphatase / :
Similarity search - Component
Biological speciesFrancisella tularensis subsp. novicida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsFelts, R.L. / Reilly, T.J. / Tanner, J.J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure of Francisella tularensis AcpA: prototype of a unique superfamily of acid phosphatases and phospholipases C
Authors: Felts, R.L. / Reilly, T.J. / Tanner, J.J.
History
DepositionAug 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: acid phosphatase
B: acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,46411
Polymers112,6782
Non-polymers1,7869
Water9,908550
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-6 kcal/mol
Surface area31800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.081, 144.399, 123.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein acid phosphatase /


Mass: 56338.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. novicida (bacteria)
Species: Francisella tularensis / Strain: subsp. novicida / Gene: acpA / Plasmid: pET20b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q2A5P7, UniProt: A0Q436*PLUS, acid phosphatase

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Non-polymers , 7 types, 559 molecules

#2: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#5: Chemical ChemComp-ETX / 2-ETHOXYETHANOL / 2-Ethoxyethanol


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#6: Chemical ChemComp-DVT / DECAVANADATE / Sodium decavanadate


Mass: 957.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O28V10
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 1500, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11601
21601
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111.127129
SYNCHROTRONAPS 19-ID21.6531
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJul 1, 2004
SBC-32CCDAug 1, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystalSINGLE WAVELENGTHMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.1271291
21.65311
ReflectionRedundancy: 14.4 % / Number: 39861 / Rmerge(I) obs: 0.065 / Χ2: 0.985 / D res high: 2.39 Å / D res low: 50 Å / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.392.4810010.1180.93413.4
5.15509910.0561.06713.7
4.095.1510010.0560.87914.4
3.574.0910010.0590.86814.6
3.243.5710010.0661.00114.6
3.013.2410010.0720.91714.6
2.833.0110010.0781.05414.6
2.692.8310010.0861.08114.5
2.572.6910010.0971.08114.5
2.482.5710010.1070.96214.5
ReflectionResolution: 1.75→50 Å / Num. obs: 98137 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.047 / Χ2: 1.015
Reflection shellResolution: 1.75→1.81 Å / % possible obs: 94.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.357 / Num. measured obs: 9497 / Χ2: 0.975

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.75 Å / D res low: 44.23 Å / FOM acentric: 0.364 / FOM centric: 0.489 / Reflection acentric: 92746 / Reflection centric: 5082
Phasing dm shellResolution: 1.75→50 Å / Delta phi final: 0.29 / FOM : 0.315 / Reflection: 98049

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
REFMACrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.75→44.28 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.27 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4923 5 %RANDOM
Rwork0.198 ---
all0.2 ---
obs-98094 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20 Å20 Å2
2---0.91 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.75→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7511 0 90 550 8151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217873
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.94910838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7755959
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.98925.602407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.025151171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9241514
X-RAY DIFFRACTIONr_chiral_restr0.0960.21089
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026210
X-RAY DIFFRACTIONr_nbd_refined0.2010.24073
X-RAY DIFFRACTIONr_nbtor_refined0.3070.25213
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2682
X-RAY DIFFRACTIONr_metal_ion_refined0.1980.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.218
X-RAY DIFFRACTIONr_mcbond_it0.4991.54846
X-RAY DIFFRACTIONr_mcangle_it0.77727659
X-RAY DIFFRACTIONr_scbond_it1.3933480
X-RAY DIFFRACTIONr_scangle_it1.8854.53115
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 358 -
Rwork0.244 6642 -
all-7000 -
obs--100 %
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)
10.9651-0.3398-0.17480.8885-0.03031.54830.04660.06150.00320.0365-0.0175-0.07130.1820.1939-0.0291-0.20370.0256-0.0402-0.1203-0.0214-0.122643.689438.93965.6175
20.6696-0.2177-0.21592.2039-0.17250.7484-0.0251-0.02690.08120.82050.09920.2248-0.2583-0.0869-0.07410.1870.05580.1165-0.11540.0179-0.099624.083667.520327.1085
39.4024-6.3033-2.99649.7998-2.00775.8684-0.0382-0.03150.02040.36070.20620.5981-0.5267-0.2188-0.168-0.1974-0.01960.0612-0.10670.0232-0.066621.14396.499912.8641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 4895 - 489
2X-RAY DIFFRACTION2BB6 - 4896 - 489
3X-RAY DIFFRACTION3BG2001

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