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- PDB-3pct: Structure of the class C acid phosphatase from Pasteurella multocida -

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Basic information

Entry
Database: PDB / ID: 3pct
TitleStructure of the class C acid phosphatase from Pasteurella multocida
ComponentsClass C acid phosphatase
KeywordsHYDROLASE / outer membrane
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
5-nucleotidase lipoprotein e(P4) / Acid phosphatase, class B-like / HAD superfamily, subfamily IIIB (Acid phosphatase) / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-nucleotidase, lipoprotein e(P4) family
Similarity search - Component
Biological speciesPasteurella multocida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSingh, H. / Malinski, T.J. / Reilly, T.J. / Tanner, J.J.
CitationJournal: Arch.Biochem.Biophys. / Year: 2011
Title: Crystal structure and immunogenicity of the class C acid phosphatase from Pasteurella multocida.
Authors: Singh, H. / Malinski, T.J. / Reilly, T.J. / Henzl, M.T. / Tanner, J.J.
History
DepositionOct 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class C acid phosphatase
B: Class C acid phosphatase
C: Class C acid phosphatase


Theoretical massNumber of molelcules
Total (without water)87,3023
Polymers87,3023
Non-polymers00
Water10,323573
1
A: Class C acid phosphatase
B: Class C acid phosphatase


Theoretical massNumber of molelcules
Total (without water)58,2012
Polymers58,2012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-40 kcal/mol
Surface area20540 Å2
MethodPISA
2
C: Class C acid phosphatase

C: Class C acid phosphatase


Theoretical massNumber of molelcules
Total (without water)58,2012
Polymers58,2012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5900 Å2
ΔGint-40 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.980, 106.150, 89.750
Angle α, β, γ (deg.)90.000, 93.110, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-502-

HOH

21C-515-

HOH

31C-573-

HOH

DetailsThe asymmetric unit contains a dimer formed by chains A and B. There is a third molecule in the asymmetric unit (chain C), and rotation of it around the crystallographic 2-fold axis (-x, y, -z) followed by translation of (1, 0, 0) generates the CC dimer.

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Components

#1: Protein Class C acid phosphatase


Mass: 29100.637 Da / Num. of mol.: 3 / Fragment: UNP residues 21-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pasteurella multocida (bacteria) / Gene: acpC / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: B9VWB2, acid phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / 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: 2.18 Å3/Da / Density % sol: 43.55 %
Crystal growTemperature: 293 K / pH: 7
Details: 20% (w/v) PEG 3350, 0.2 M ammonium citrate, and 10% (v/v) n-propanol, pH 7, temperature 293K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→26.616 Å / Num. all: 62294 / Num. obs: 62294 / % possible obs: 97.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.952.50.2722.41988980500.27286.7
1.95-2.073.20.252.72779186210.2598.3
2.07-2.213.70.1813.73019682500.181100
2.21-2.393.60.1494.32802676840.14999.9
2.39-2.623.70.1165.42593970500.11699.9
2.62-2.933.70.0976.32362464040.09799.9
2.93-3.383.70.0827.42100456620.08299.9
3.38-4.143.70.0747.91780947940.07499.9
4.14-5.853.70.0688.51388737280.068100
5.85-27.5173.70.0658751920510.06599

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data processing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ET4

3et4


Resolution: 1.85→26.616 Å / Occupancy max: 1 / Occupancy min: 0.02 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2672 3141 5.04 %random
Rwork0.2117 ---
obs0.2145 62271 97.72 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.529 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 106.97 Å2 / Biso mean: 23.5014 Å2 / Biso min: 3.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.5149 Å20 Å2-6.4284 Å2
2--0.4749 Å20 Å2
3----2.9897 Å2
Refinement stepCycle: LAST / Resolution: 1.85→26.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5764 0 0 573 6337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065947
X-RAY DIFFRACTIONf_angle_d0.9398054
X-RAY DIFFRACTIONf_chiral_restr0.072851
X-RAY DIFFRACTIONf_plane_restr0.0041071
X-RAY DIFFRACTIONf_dihedral_angle_d14.6032090
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.87890.38291220.30452187230981
1.8789-1.90970.3231260.26792384251086
1.9097-1.94260.31711100.24822492260291
1.9426-1.97790.29891460.26292588273495
1.9779-2.0160.32361270.25012749287698
2.016-2.05710.30161470.243527082855100
2.0571-2.10180.32721450.235727482893100
2.1018-2.15070.29341430.23127632906100
2.1507-2.20450.29541540.221727332887100
2.2045-2.2640.32181520.22327152867100
2.264-2.33060.29571300.210827462876100
2.3306-2.40580.31211410.206627512892100
2.4058-2.49170.29041510.217127492900100
2.4917-2.59140.29261470.211227252872100
2.5914-2.70920.26081360.213427582894100
2.7092-2.85190.27941430.224227632906100
2.8519-3.03040.25481490.216527722921100
3.0304-3.2640.26751370.217927342871100
3.264-3.59170.25371580.206227422900100
3.5917-4.10980.21861640.180427562920100
4.1098-5.17170.20811500.166327682918100
5.1717-26.61850.23151630.198127992962100
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)
10.452-0.14160.29330.2876-0.0520.4579-0.0783-0.04090.10290.02080.0163-0.0226-0.01-0.09680.05770.0493-0.0431-0.02190.08140.01580.072820.986124.099131.7782
20.2822-0.05050.35840.1736-0.09090.46990.03430.0488-0.021-0.0265-0.0138-0.00450.10520.0807-0.01690.0857-0.0414-0.01240.08210.03460.038631.29873.092425.6879
30.2024-0.11870.27460.4689-0.29950.69690.06240.0737-0.0189-0.0838-0.09880.02140.13780.13050.03040.04760.0211-0.00790.03790.02310.03548.414863.4272-8
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA3 - 253
2X-RAY DIFFRACTION2chain BB6 - 259
3X-RAY DIFFRACTION3chain CC3 - 259

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