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- PDB-5xwi: Crystal Structure of SPAP, an alkaline phosphatase from Sphingomo... -

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Basic information

Entry
Database: PDB / ID: 5xwi
TitleCrystal Structure of SPAP, an alkaline phosphatase from Sphingomonas showing covalent intermediate
ComponentsAlkaline phosphatase PhoK
KeywordsHYDROLASE / alkaline phosphatase / reaction intermediate
Function / homology
Function and homology information


alkaline phosphatase / alkaline phosphatase activity / dephosphorylation / zinc ion binding / extracellular region / metal ion binding
Similarity search - Function
Gyrase A; domain 2 - #150 / Alkaline phosphatase, prokaryotic / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / Gyrase A; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alkaline phosphatase PhoK
Similarity search - Component
Biological speciesSphingomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.872 Å
AuthorsBihani, S.C.
CitationJournal: To Be Published
Title: Crystal Structure of SPAP, an alkaline phosphatase from Sphingomonas showing covalent intermediate
Authors: Bihani, S.C.
History
DepositionJun 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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_conn_type
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_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_symmetry / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkaline phosphatase PhoK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5596
Polymers61,2001
Non-polymers3595
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-56 kcal/mol
Surface area18750 Å2
Unit cell
Length a, b, c (Å)87.600, 87.600, 168.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-951-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alkaline phosphatase PhoK / SPAP protein


Mass: 61200.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. (bacteria) / Gene: phoK / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A1YYW7, alkaline phosphatase

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Non-polymers , 5 types, 291 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 53.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.6M Ammonium Sulfate 100mM MES Buffer, pH 6.5, 1mM pNPP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979576 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979576 Å / Relative weight: 1
ReflectionResolution: 1.87→42.4 Å / Num. obs: 54473 / % possible obs: 99.3 % / Redundancy: 4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.56
Reflection shellResolution: 1.87→1.98 Å / Redundancy: 4.04 % / Rmerge(I) obs: 0.68 / CC1/2: 0.69 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q3Q

3q3q


Resolution: 1.872→42.384 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.59
RfactorNum. reflection% reflection
Rfree0.2102 2720 5 %
Rwork0.1716 --
obs0.1735 54407 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.872→42.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 14 286 4066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073880
X-RAY DIFFRACTIONf_angle_d1.0955285
X-RAY DIFFRACTIONf_dihedral_angle_d12.7771393
X-RAY DIFFRACTIONf_chiral_restr0.04587
X-RAY DIFFRACTIONf_plane_restr0.005698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8719-1.9060.29391400.25432660X-RAY DIFFRACTION98
1.906-1.94260.26711400.23952657X-RAY DIFFRACTION100
1.9426-1.98230.26941410.21492676X-RAY DIFFRACTION100
1.9823-2.02540.24211420.21442704X-RAY DIFFRACTION100
2.0254-2.07250.25941390.21712651X-RAY DIFFRACTION99
2.0725-2.12430.23981420.18942696X-RAY DIFFRACTION100
2.1243-2.18180.20661430.17662716X-RAY DIFFRACTION100
2.1818-2.2460.22071430.16582712X-RAY DIFFRACTION100
2.246-2.31850.17791410.16612672X-RAY DIFFRACTION100
2.3185-2.40130.24761420.15992707X-RAY DIFFRACTION100
2.4013-2.49750.18791430.16392711X-RAY DIFFRACTION100
2.4975-2.61110.21871430.17242728X-RAY DIFFRACTION100
2.6111-2.74870.22391440.16392724X-RAY DIFFRACTION100
2.7487-2.92090.22151440.1712733X-RAY DIFFRACTION100
2.9209-3.14640.20051440.18072741X-RAY DIFFRACTION100
3.1464-3.46290.21851450.16152752X-RAY DIFFRACTION100
3.4629-3.96370.18181470.15432790X-RAY DIFFRACTION100
3.9637-4.99250.16311480.14282815X-RAY DIFFRACTION100
4.9925-42.39460.22591490.18332842X-RAY DIFFRACTION95
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)
11.7453-1.13610.31951.3697-0.96741.9741-0.12110.05470.08090.13360.0535-0.0275-0.1614-0.07640.04940.1901-0.0639-0.05430.23280.05320.2034-0.498317.2915-5.2875
21.36621.4146-0.23792.50851.4092.69120.27140.2059-0.3629-0.4762-0.16770.40420.1006-0.3792-0.07510.3168-0.044-0.21160.4828-0.00740.4364-17.17219.5052-27.9431
31.9173-0.5375-0.12212.09040.00961.8308-0.06780.13480.03390.02180.09970.2096-0.195-0.43350.01310.1716-0.0073-0.05240.39130.09310.2536-14.376724.3667-15.4255
46.1385-1.0328-1.91321.68950.25480.6031-0.03770.73840.5786-0.0642-0.1664-0.2931-0.3160.24680.18750.2443-0.0658-0.07970.54440.20960.3223-3.049429.5622-27.9864
50.7077-0.10510.49671.2215-1.79892.82570.14260.62390.2071-0.3498-0.3793-0.17580.19980.80330.29460.25920.08360.0370.72740.19420.329418.854711.724-21.6406
62.5253-1.5142-1.2480.92810.61762.47620.11450.73570.3714-0.1531-0.3706-0.2806-0.21340.25890.19660.2132-0.0519-0.04770.54910.18850.31187.621323.1702-23.8561
71.4311-0.98320.79770.988-0.82091.7577-0.04610.34950.28850.0808-0.1753-0.1845-0.19430.18970.16350.1805-0.0873-0.06370.280.09670.23734.583320.2234-12.8793
80.70050.12690.32310.0721-0.08350.55740.19640.3524-0.4672-0.469-0.00880.41150.6543-0.044-0.22490.6592-0.1131-0.3610.4151-0.11440.5726-6.9886-8.626-21.9912
91.4462-0.44171.06970.5152-0.39190.79120.3040.1072-0.3995-0.22580.0790.42670.5545-0.3347-0.08160.3449-0.2043-0.17740.39090.06810.4858-9.9937-2.7707-12.1324
101.7371-1.20380.57662.4485-0.09872.7045-0.2181-0.1112-0.02840.36260.21620.2035-0.2332-0.39440.02950.2154-0.0146-0.01420.25040.07540.201-5.862516.99840.2186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 140 )
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 184 )
4X-RAY DIFFRACTION4chain 'A' and (resid 185 through 218 )
5X-RAY DIFFRACTION5chain 'A' and (resid 219 through 245 )
6X-RAY DIFFRACTION6chain 'A' and (resid 246 through 280 )
7X-RAY DIFFRACTION7chain 'A' and (resid 281 through 357 )
8X-RAY DIFFRACTION8chain 'A' and (resid 358 through 424 )
9X-RAY DIFFRACTION9chain 'A' and (resid 425 through 487 )
10X-RAY DIFFRACTION10chain 'A' and (resid 488 through 556 )

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