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- PDB-4e3w: Crystal Structure Francisella tularensis histidine acid phosphata... -

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Basic information

Entry
Database: PDB / ID: 4e3w
TitleCrystal Structure Francisella tularensis histidine acid phosphatase cryoprotected with proline
ComponentsAcid phosphatase
KeywordsHYDROLASE
Function / homologyPhosphoglycerate mutase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / PROLINE / :
Function and homology information
Biological speciesFrancisella tularensis subsp. holarctica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsTanner, J.J. / Pemberton, T.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Proline: Mother Nature's cryoprotectant applied to protein crystallography.
Authors: Pemberton, T.A. / Still, B.R. / Christensen, E.M. / Singh, H. / Srivastava, D. / Tanner, J.J.
History
DepositionMar 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,6828
Polymers77,0682
Non-polymers6156
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-95 kcal/mol
Surface area26000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.031, 62.031, 210.411
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


Mass: 38533.945 Da / Num. of mol.: 2 / Fragment: UNP residues 17-351 / Mutation: H17N, D261A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. holarctica (bacteria)
Strain: LVS / Gene: FTL_0031 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2A612, acid phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.0M ammonium sulfate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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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: Dec 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→43.863 Å / Num. all: 78960 / Num. obs: 78960 / % possible obs: 99.1 % / Redundancy: 4.3 % / Rsym value: 0.032 / Net I/σ(I): 25.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.842.80.13631046110390.1395.3
1.84-1.963.20.1086.934925109160.10899.1
1.96-2.093.40.0751035421102970.07599.8
2.09-2.263.60.056133466396100.05699.8
2.26-2.473.80.04715.33374588460.04799.9
2.47-2.774.40.0417.33505379960.0499.9
2.77-3.25.70.03419.64053770750.034100
3.2-3.917.10.02921.84259059700.029100
3.91-5.537.40.02524.53426646410.025100
5.53-43.8637.40.0225.31906625700.0299.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IT2

3it2


Resolution: 1.75→43.863 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.8847 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 19.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2025 3963 5.03 %
Rwork0.1818 --
obs0.1828 78805 99.01 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.824 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso max: 57.9 Å2 / Biso mean: 19.7208 Å2 / Biso min: 5.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.6077 Å20 Å2-0 Å2
2--0.6077 Å20 Å2
3----0.135 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5027 0 36 365 5428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065179
X-RAY DIFFRACTIONf_angle_d1.0077054
X-RAY DIFFRACTIONf_chiral_restr0.069794
X-RAY DIFFRACTIONf_plane_restr0.004905
X-RAY DIFFRACTIONf_dihedral_angle_d11.1061864
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.77140.27751460.21272495264192
1.7714-1.79380.25261380.20062514265295
1.7938-1.81740.2481240.192625274996
1.8174-1.84230.21721520.18412582273498
1.8423-1.86860.25651370.17592719285699
1.8686-1.89650.22141420.18532658280099
1.8965-1.92620.25041280.21312670279897
1.9262-1.95770.19971340.182626622796100
1.9577-1.99150.21391490.165126902839100
1.9915-2.02770.19671460.162226732819100
2.0277-2.06670.22181450.173827352880100
2.0667-2.10890.21141370.184426572794100
2.1089-2.15470.20741460.173926852831100
2.1547-2.20490.19061390.175527352874100
2.2049-2.260.21441410.18592643278499
2.26-2.32110.19711490.17322649279899
2.3211-2.38940.20051440.176927332877100
2.3894-2.46650.22631390.182926742813100
2.4665-2.55470.22531400.184526742814100
2.5547-2.65690.2081360.195327412877100
2.6569-2.77780.21451500.192626792829100
2.7778-2.92430.22171560.189827132869100
2.9243-3.10740.181300.194326862816100
3.1074-3.34730.20981560.199126852841100
3.3473-3.6840.18481540.175826962850100
3.684-4.21670.16041250.162827302855100
4.2167-5.31110.15111460.154727012847100
5.3111-43.8630.23281340.199827382872100
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)
10.8568-0.1221-0.92370.6580.18681.18350.019-0.2036-0.0202-0.01480.0366-0.0825-0.01280.3056-0.02660.0777-0.02550.0080.1831-0.02240.04049.591215.9265-1.4841
20.7308-0.1311-0.19150.7940.94811.17240.0413-0.00580.0844-0.20630.02380.0079-0.30990.0201-0.02650.1897-0.02970.02510.0698-0.00730.0244-15.076140.57721.1569
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 6:334 )A6 - 334
2X-RAY DIFFRACTION2( CHAIN B AND RESID 6:334 )B6 - 334

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