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- PDB-4nx8: Structure of a PTP-like phytase from Bdellovibrio bacteriovorus -

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Basic information

Entry
Database: PDB / ID: 4nx8
TitleStructure of a PTP-like phytase from Bdellovibrio bacteriovorus
ComponentsProtein-tyrosine phosphatase 2
KeywordsHYDROLASE / PTP-like phytase / phytase / inositol phosphatase / protein tyrosine phosphatase
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / metal ion binding
Similarity search - Function
Inositol hexakisphosphate / Inositol hexakisphosphate / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Inositol hexakisphosphate / Inositol hexakisphosphate / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Protein-tyrosine phosphatase 2
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 Å
AuthorsGruninger, R.J. / Lovering, A.L.
CitationJournal: Plos One / Year: 2014
Title: Structural and biochemical analysis of a unique phosphatase from Bdellovibrio bacteriovorus reveals its structural and functional relationship with the protein tyrosine phosphatase class of phytase.
Authors: Gruninger, R.J. / Thibault, J. / Capeness, M.J. / Till, R. / Mosimann, S.C. / Sockett, R.E. / Selinger, B.L. / Lovering, A.L.
History
DepositionDec 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Protein-tyrosine phosphatase 2
B: Protein-tyrosine phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3666
Polymers67,2012
Non-polymers1654
Water10,106561
1
A: Protein-tyrosine phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7414
Polymers33,6001
Non-polymers1413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein-tyrosine phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6252
Polymers33,6001
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.640, 78.560, 69.820
Angle α, β, γ (deg.)90.000, 93.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein-tyrosine phosphatase 2


Mass: 33600.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (bacteria) / Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: Bd1204 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6MNP0, protein-tyrosine-phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200 mM MgCl2, 100 mM Tris-HCl (7.0), 8-10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 10, 2010
RadiationMonochromator: ACCEL/BRUKER double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.698→34.222 Å / Num. all: 63333 / Num. obs: 63333 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.078 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.698-1.793.10.4331.42725588580.43394.7
1.79-1.93.40.2841.52953387120.284100
1.9-2.033.40.1773.32811782750.177100
2.03-2.193.40.1195.52632677200.119100
2.19-2.43.40.1024.12414170600.102100
2.4-2.683.40.08182213064500.081100
2.68-3.13.40.0728.71943056530.072100
3.1-3.83.40.07681661448230.076100
3.8-5.373.40.061101282837290.06199.8
5.37-34.2223.40.0549.6688220530.05498.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PSZ

2psz


Resolution: 1.698→34.222 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.21 / σ(F): 1.35 / σ(I): 1.5 / Phase error: 19.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1928 3211 5.07 %Random
Rwork0.1563 ---
all0.1585 63333 --
obs0.1581 63305 99.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.04 Å2 / Biso mean: 31.8236 Å2 / Biso min: 13.61 Å2
Refinement stepCycle: LAST / Resolution: 1.698→34.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4241 0 9 561 4811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174440
X-RAY DIFFRACTIONf_angle_d1.6486036
X-RAY DIFFRACTIONf_chiral_restr0.086643
X-RAY DIFFRACTIONf_plane_restr0.009787
X-RAY DIFFRACTIONf_dihedral_angle_d13.9621697
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.698-1.72340.30511260.27662308243488
1.7234-1.75030.32321330.26642471260494
1.7503-1.7790.25931540.240926172771100
1.779-1.80970.31311420.212226062748100
1.8097-1.84260.2711420.19726542796100
1.8426-1.8780.21911590.185825622721100
1.878-1.91630.22721480.166526132761100
1.9163-1.9580.21941280.155426422770100
1.958-2.00350.18871370.156126252762100
2.0035-2.05360.19541220.165426772799100
2.0536-2.10920.22271350.165526172752100
2.1092-2.17120.1851340.152826152749100
2.1712-2.24130.18561350.147126592794100
2.2413-2.32140.21611450.156226332778100
2.3214-2.41430.20431580.157225872745100
2.4143-2.52410.21781190.150526662785100
2.5241-2.65720.19241470.161826182765100
2.6572-2.82360.21621310.162126652796100
2.8236-3.04150.17871270.148426482775100
3.0415-3.34730.17461670.147126212788100
3.3473-3.83110.1781410.140426482789100
3.8311-4.82460.15531380.131926532791100
4.8246-34.22880.17021430.15882689283299
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)
10.29280.2232-0.0190.49510.02620.2139-0.16010.2360.2467-0.23430.20290.2321-0.14430.0458-0.06410.2699-0.0801-0.05460.33090.05670.208318.0521-19.435516.2027
20.15730.0514-0.01740.1075-0.02090.0638-0.13820.16280.1847-0.16230.12960.1662-0.16310.0173-0.00470.1797-0.0369-0.01120.18710.02870.220817.5591-21.318524.4126
30.0354-0.026-0.06080.1513-0.01160.1015-0.0689-0.03650.0057-0.0127-0.01970.1012-0.0315-0.082100.1538-0.00570.00090.18610.00520.216213.0532-30.38430.8358
40.21520.13440.14620.30010.07910.2777-0.17090.27080.0236-0.26030.24670.0994-0.06520.13360.0320.2416-0.07560.01270.25340.01460.184527.7601-19.752316.7915
50.122-0.0326-0.03160.08260.01210.01260.00750.18920.129-0.3330.1202-0.0297-0.11910.08010.12380.833-0.4467-0.02080.48990.35370.135130.2108-5.34246.3408
60.17060.05880.02270.02260.01710.03470.06560.19970.2518-0.03740.13480.1169-0.0943-0.0471-0.00410.74180.0473-0.10940.2950.13540.743719.38081.219820.5721
70.56170.10180.18750.13270.24930.7322-0.18160.3360.2594-0.29520.2319-0.0512-0.39540.5212-0.04880.3336-0.15210.03940.26380.02090.237636.9697-7.604920.1358
80.0589-0.02280.05050.1701-0.06190.0339-0.0949-0.1215-0.3320.04880.0860.25710.1890.0382-0.00210.22250.04080.02780.27530.04110.266643.207-18.945144.8524
90.06480.06940.03330.1834-0.03020.0735-0.0884-0.46370.00730.26970.13030.08010.15460.0658-0.00740.36540.12660.0520.43570.01250.178646.1142-12.518661.8371
100.0780.0159-0.02710.0379-0.00030.018-0.1796-0.37230.01940.24560.18670.0338-0.0828-0.12070.00480.27980.1208-0.01270.3218-0.03690.173749.7571-9.325456.2243
110.07280.04250.00330.0237-0.01650.0242-0.0151-0.1428-0.15280.0887-0.03830.11560.1224-0.1146-0.00010.1980.01390.03630.1820.00890.247638.0017-12.624743.9059
120.0341-0.02060.02120.01810.00860.02440.02050.08070.0158-0.0958-0.021-0.0497-0.00560.0518-00.18720.00620.00460.18430.01160.215648.0711-10.853436.4361
130.0582-0.10730.02290.1670.14820.2758-0.0461-0.14620.01020.12070.04150.08280.0224-0.0462-0.00030.14620.0395-0.00010.1687-0.00970.181148.4872-9.165947.0131
140.2907-0.17720.1650.5416-0.05450.2002-0.2302-0.5181-0.07060.39810.20710.11790.08360.08290.03780.32210.1084-0.01160.3350.02440.151554.1312-17.546257.5012
150.11130.07430.050.05910.04480.03740.1097-0.1716-0.12140.1790.05610.02840.1646-0.02660.15270.62310.29390.00010.56010.38130.119257.0982-28.910363.5065
160.02010.00280.01140.00380.00050.00720.0575-0.3104-0.3210.03070.04530.12840.0506-0.03230.00020.6793-0.0270.0030.32560.11590.639346.2654-35.651749.4356
170.2238-0.0644-0.2040.01670.06230.1895-0.1013-0.286-0.35540.19170.13410.02490.29710.2431-0.13270.40550.1638-0.02680.17630.09110.28858.7878-30.46349.5794
180.05810.0417-0.03450.0398-0.03810.0359-0.0868-0.16170.12440.1625-0.0438-0.3151-0.06090.2812-0.0050.30230.1101-0.07210.4593-0.0540.256770.5772-21.968149.899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 91 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 127 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 158 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 159 through 225 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 226 through 242 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 243 through 257 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 258 through 293 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 33 through 62 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 63 through 84 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 85 through 104 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 105 through 120 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 121 through 141 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 142 through 194 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 195 through 225 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 226 through 242 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 243 through 257 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 258 through 278 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 279 through 293 )B0

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