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- PDB-3it0: Crystal Structure Francisella tularensis histidine acid phosphata... -

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Basic information

Entry
Database: PDB / ID: 3it0
TitleCrystal Structure Francisella tularensis histidine acid phosphatase complexed with phosphate
ComponentsAcid phosphatase
KeywordsHYDROLASE / Histidine Acid Phosphatase / HAP
Function / homologyPhosphoglycerate mutase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHATE ION / :
Function and homology information
Biological speciesFrancisella tularensis subsp. holarctica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.692 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 1.2Sep 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 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,1118
Polymers77,2042
Non-polymers9076
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-35 kcal/mol
Surface area25690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.640, 61.640, 211.320
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: 38601.996 Da / Num. of mol.: 2 / Fragment: UNP residues 17-351
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 52.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.05 - 0.20 M Bis-Tris buffer pH 5.0 - 6.5, 17 -25 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 17, 2009
RadiationMonochromator: beamline optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.692→34.95 Å / Num. obs: 86186 / % possible obs: 99 % / Redundancy: 4.08 % / Rmerge(I) obs: 0.095 / Χ2: 0.95 / Net I/σ(I): 8.4 / Scaling rejects: 2657
Reflection shellResolution: 1.692→1.76 Å / Redundancy: 3.12 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 2.9 / Num. measured all: 26011 / Num. unique all: 8325 / Χ2: 0.79 / % possible all: 95.1

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
d*TREKdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IT1

3it1


Resolution: 1.692→34.857 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.848 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 4369 5.07 %based on test set used for refinement of the tartrate complex of this enzyme
Rwork0.189 ---
obs0.191 86179 98.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.102 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 86.07 Å2 / Biso mean: 28.458 Å2 / Biso min: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.692→34.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5042 0 52 516 5610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045268
X-RAY DIFFRACTIONf_angle_d0.9057164
X-RAY DIFFRACTIONf_chiral_restr0.059799
X-RAY DIFFRACTIONf_plane_restr0.004918
X-RAY DIFFRACTIONf_dihedral_angle_d16.2391892
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 (%)
1.692-1.7110.2711330.2142445257887
1.711-1.7310.2331430.2062575271896
1.731-1.7530.2521670.2142661282896
1.753-1.7750.2451410.1952648278997
1.775-1.7980.2061490.2062659280897
1.798-1.8230.2181290.1912752288198
1.823-1.8490.2721630.1992673283698
1.849-1.8760.251320.2042714284699
1.876-1.9060.2271410.192726286799
1.906-1.9370.2471430.1942803294699
1.937-1.970.2171380.19127402878100
1.97-2.0060.2621580.19127312889100
2.006-2.0450.2531440.19827762920100
2.045-2.0860.2131460.18627662912100
2.086-2.1320.1931510.18427592910100
2.132-2.1810.1961380.18627592897100
2.181-2.2360.1971500.17327412891100
2.236-2.2960.2141540.19128042958100
2.296-2.3640.2321410.18427602901100
2.364-2.440.2231500.19427132863100
2.44-2.5270.2351380.19827772915100
2.527-2.6280.2461450.20127732918100
2.628-2.7480.2051440.19927512895100
2.748-2.8930.2241720.19227612933100
2.893-3.0740.2211310.19827772908100
3.074-3.3110.2261550.20427522907100
3.311-3.6440.1991600.17727832943100
3.644-4.1710.1881270.16627622889100
4.171-5.2520.1321490.15327652914100
5.252-34.8650.2161370.1852704284196
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)
10.7579-0.0543-0.71830.73390.20340.6162-0.0095-0.1887-0.0518-0.03770.0377-0.0653-0.01130.2127-0.02710.1719-0.03270.01690.266-0.01510.06369.437315.743-1.3645
20.7238-0.0042-0.1910.76780.75170.63120.0369-0.03680.0631-0.191-0.00940.0489-0.210.0122-0.02520.272-0.02680.01640.1815-0.01780.0701-15.049440.2361.3571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA6 - 334
2X-RAY DIFFRACTION2chain BB6 - 334

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