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- PDB-4etm: Crystal structure of YfkJ from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 4etm
TitleCrystal structure of YfkJ from Bacillus subtilis
ComponentsLow molecular weight protein-tyrosine-phosphatase yfkJ
KeywordsHYDROLASE / Tyrosine Phosphatase / Dephosphorylation
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity
Similarity search - Function
Protein-tyrosine phosphatase, low molecular weight / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Low molecular weight protein-tyrosine-phosphatase YfkJ
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCao, X.F. / Su, X.D.
CitationJournal: To be published
Title: Crystal structure of YfkJ from Bacillus subtilis
Authors: Cao, X.F. / Su, X.D.
History
DepositionApr 24, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_ref_seq_dif / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

Downloads & links

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Assembly

Deposited unit
A: Low molecular weight protein-tyrosine-phosphatase yfkJ
B: Low molecular weight protein-tyrosine-phosphatase yfkJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2178
Polymers37,9032
Non-polymers3146
Water7,981443
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.152, 52.922, 86.609
Angle α, β, γ (deg.)90.00, 102.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-439-

HOH

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Components

#1: Protein Low molecular weight protein-tyrosine-phosphatase yfkJ / LMPTP


Mass: 18951.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yfkJ, BSU07880 / Production host: Escherichia coli (E. coli) / References: UniProt: O35016, protein-tyrosine-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.05
Details: 1.344M dipotassium phosphate, 0.056M monosodium phosphate, pH 8.05, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 15, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 40047 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3
Reflection shellResolution: 1.6→1.63 Å / % possible all: 98.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5PNT

5pnt


Resolution: 1.6→21.368 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 2008 5.01 %RANDOM
Rwork0.2247 ---
obs0.226 40042 97.74 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.86 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.5031 Å2-0 Å2-0.6435 Å2
2---0.6955 Å2-0 Å2
3----2.8076 Å2
Refinement stepCycle: LAST / Resolution: 1.6→21.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2443 0 14 443 2900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072498
X-RAY DIFFRACTIONf_angle_d1.113361
X-RAY DIFFRACTIONf_dihedral_angle_d13.412931
X-RAY DIFFRACTIONf_chiral_restr0.078366
X-RAY DIFFRACTIONf_plane_restr0.004443
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6002-1.64020.30441430.3074274099
1.6402-1.68450.30251330.28342766100
1.6845-1.73410.32691530.26472728100
1.7341-1.790.32591380.2762275299
1.79-1.8540.28651340.2359275098
1.854-1.92820.44261060.3747262493
1.9282-2.01590.29311250.2649261095
2.0159-2.12210.32271140.3119261293
2.1221-2.25490.281430.2512265897
2.2549-2.42870.22951680.2259273899
2.4287-2.67270.26411810.20572726100
2.6727-3.05850.21541460.19772771100
3.0585-3.84970.21351470.1725277999
3.8497-21.36950.19051770.1759278598
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)
10.27130.13640.25670.0924-0.08972.1110.211-0.39310.18090.2790.0498-0.0686-0.01910.230.20090.64660.20950.10540.5021-0.1315-0.1058-0.9963-13.3485-53.4392
20.9359-0.0432-0.41710.96050.20781.50090.11970.3981-0.0254-0.2115-0.12350.0942-0.0003-0.0739-0.01570.13470.06180.00680.1950.00010.1219-8.448-8.1755-35.7969
30.24730.4114-0.71020.6497-1.21434.360.06260.46250.0554-0.4373-0.05290.07760.1335-0.2171-0.04380.30740.0377-0.01970.3072-0.02530.1205-6.6998-12.401-42.8845
41.2272-0.0471-0.15592.2607-0.11161.06570.08810.2409-0.1214-0.2214-0.03510.40710.0727-0.39940.02210.09070.0228-0.00960.2014-0.00190.1661-15.3178-11.1238-29.4869
50.68680.27-0.36141.03870.51451.4489-0.09230.2681-0.25460.081-0.0659-0.27580.56140.24420.08480.21550.10080.02990.2175-0.01750.18661.3175-15.4291-33.9475
62.0697-2.4424-0.33535.47041.26531.59970.1265-0.0417-0.47550.21480.0147-0.54410.1562-0.0097-0.12010.1108-0.0285-0.03170.13170.00110.2564.3359-13.1904-24.1584
71.4025-1.24390.13792.0193-0.43020.94520.18620.32420.0654-0.0142-0.3317-0.50660.03280.33620.07930.15930.01580.01540.23050.04010.23396.9828-11.1309-31.6677
81.96350.1547-2.10960.2832-0.47545.25460.25710.04450.6858-0.01520.0101-0.2803-1.00030.2374-0.05960.3339-0.05150.00820.15660.02660.32510.05542.0191-28.7068
90.56620.34-0.12280.7353-0.11491.1272-0.1678-0.17340.00570.68210.2527-0.06860.0510.1353-0.09910.31810.10840.04750.185-0.00630.1926-11.8284-2.9326-19.1437
102.66450.0087-1.77261.31920.80083.65310.04440.53580.1793-0.2983-0.1191-0.1773-0.3288-0.02470.04310.24130.04190.03330.24660.0840.1751-3.644-0.6694-38.6279
110.04660.0347-0.27210.27760.74943.0385-0.0028-0.0553-0.01770.101-0.0534-0.04670.40440.09750.01110.1545-0.00230.01610.13910.00780.118914.9349-12.436-5.0205
121.54270.06340.22561.4433-0.00172.06180.0723-0.1796-0.04260.1983-0.0013-0.1490.02860.1773-0.03920.124-0.0012-0.02110.12760.01130.125520.0293-10.9582-8.8625
132.26080.86020.43521.48050.06811.5331-0.0744-0.06910.1421-0.0840.06430.0696-0.1986-0.17420.01590.13990.0185-0.00290.10110.02020.12787.5681-6.3685-14.3046
143.19040.2873-1.56781.6788-0.12274.7775-0.0721-0.42380.29890.22830.06220.0962-0.07710.0991-0.01470.210.0147-0.01480.157-0.03850.185415.1247-0.4199-4.4758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ -7:1)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 2:29)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 30:41)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 42:75)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 76:89)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 90:100)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 101:113)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 114:125)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 126:131)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 132:156)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ -3:13)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 14:89)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 90:131)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 132:155)

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