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- PDB-3it3: Crystal Structure Francisella tularensis histidine acid phosphata... -

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Basic information

Entry
Database: PDB / ID: 3it3
TitleCrystal Structure Francisella tularensis histidine acid phosphatase D261A mutant complexed with substrate 3'-AMP
ComponentsAcid phosphatase
KeywordsHYDROLASE / Histidine Acid Phosphatase / HAP
Function / homologyPhosphoglycerate mutase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-3AM / :
Function and homology information
Biological speciesFrancisella tularensis subsp. holarctica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSingh, H. / Felts, R.L. / Reilly, T.J. / Tanner, J.J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structures of the histidine acid phosphatase from Francisella tularensis provide insight into substrate recognition.
Authors: Singh, H. / Felts, R.L. / Schuermann, J.P. / Reilly, T.J. / Tanner, J.J.
History
DepositionAug 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 1.3Oct 13, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)77,8104
Polymers77,1162
Non-polymers6942
Water10,449580
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-26 kcal/mol
Surface area28220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.646, 61.646, 211.439
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Acid phosphatase / HISTIDINE ACID PHOSPHATASE


Mass: 38557.988 Da / Num. of mol.: 2 / Fragment: UNP residues 17-351 / Mutation: D261A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. holarctica (bacteria)
Strain: LVS / Gene: FTL_0031 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21AI / References: UniProt: Q2A612, acid phosphatase
#2: Chemical ChemComp-3AM / [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate / 3'-AMP


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.05 - 0.2 M Bis-Tris buffer pH 5.0 - 6.5, 1.6 - 2.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: Q315 / Detector: CCD / Date: Jul 10, 2009
RadiationMonochromator: beamline optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 125320 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.074 / Χ2: 1.125 / Net I/σ(I): 7.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.539 / Num. unique all: 12442 / Χ2: 0.481 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IT1

3it1


Resolution: 1.5→33.63 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.899 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.187 6342 5.07 %based on test set used for refinement of the tartrate complex of this enzyme
Rwork0.172 ---
obs0.172 125177 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.415 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso max: 93.46 Å2 / Biso mean: 20.712 Å2 / Biso min: 7.64 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5220 0 46 580 5846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055478
X-RAY DIFFRACTIONf_angle_d0.9837471
X-RAY DIFFRACTIONf_chiral_restr0.064823
X-RAY DIFFRACTIONf_plane_restr0.004957
X-RAY DIFFRACTIONf_dihedral_angle_d16.9051999
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.5170.212050.18538734078100
1.517-1.5350.2072070.1939994206100
1.535-1.5540.2292100.18939234133100
1.554-1.5730.1962080.17439724180100
1.573-1.5940.2032260.17739274153100
1.594-1.6160.1882090.17440024211100
1.616-1.6390.2032020.17139504152100
1.639-1.6630.1982140.16739874201100
1.663-1.6890.1722080.16239054113100
1.689-1.7170.2022280.16439874215100
1.717-1.7470.1852250.16439584183100
1.747-1.7780.2062220.16239364158100
1.778-1.8130.1722060.1640164222100
1.813-1.850.1882190.15738754094100
1.85-1.890.1862060.16339954201100
1.89-1.9340.1742020.15239774179100
1.934-1.9820.2012020.1639624164100
1.982-2.0360.2082150.16239654180100
2.036-2.0960.1742110.16239514162100
2.096-2.1630.1862090.16439624171100
2.163-2.2410.1612140.15639784192100
2.241-2.330.1832100.16139474157100
2.33-2.4360.1832150.16239704185100
2.436-2.5650.2032100.17940134223100
2.565-2.7250.1881980.18439534151100
2.725-2.9360.1842400.17839794219100
2.936-3.2310.2011940.18339754169100
3.231-3.6980.1672270.16539294156100
3.698-4.6570.1431920.1539854177100
4.657-33.6390.2012080.1883984419299
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)
10.5614-0.0389-0.51470.57940.27850.7549-0.0048-0.0592-0.02880.04440.0455-0.06740.0240.1666-0.03240.1048-0.00090.00180.1561-0.01490.049710.271616.4296-1.2372
20.5432-0.0388-0.26420.57310.53050.72230.04560.0430.0683-0.0578-0.00670.032-0.1651-0.0211-0.03180.1626-0.00140.01770.11170.00090.0543-14.385541.2111.3591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA6 - 342
2X-RAY DIFFRACTION2chain BB5 - 342

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