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

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Basic information

Entry
Database: PDB / ID: 5xwk
TitleCrystal Structure of SPAP, an alkaline phosphatase from Sphingomonas in complex with inorganic phosphate
ComponentsAlkaline phosphatase PhoK
KeywordsHYDROLASE / alkaline phosphatase
Function / homology
Function and homology information


nucleoside triphosphate metabolic process / nucleoside triphosphate diphosphatase activity / alkaline phosphatase / alkaline phosphatase activity / vacuole / dephosphorylation / ribonucleoside triphosphate phosphatase activity / 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
PHOSPHATE ION / Alkaline phosphatase PhoK
Similarity search - Component
Biological speciesSphingomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsBihani, S.C. / Hosur, M.V.
CitationJournal: To Be Published
Title: Crystal Structure of SPAP, an alkaline phosphatase from Sphingomonas in complex with
Authors: Bihani, S.C.
History
DepositionJun 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 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
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.pdbx_dist_value / _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_symmetry

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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)61,84610
Polymers61,1201
Non-polymers7269
Water7,386410
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-72 kcal/mol
Surface area20130 Å2
Unit cell
Length a, b, c (Å)86.990, 86.990, 165.484
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-1057-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alkaline phosphatase PhoK / SPAP protein


Mass: 61120.133 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, 419 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.8M Ammonium Sulfate, 100mM Tris, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979685 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979685 Å / Relative weight: 1
ReflectionResolution: 1.9→77 Å / Num. obs: 50640 / % possible obs: 99.7 % / Redundancy: 5.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Net I/σ(I): 17.5
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.572 / CC1/2: 0.773 / % possible all: 95.7

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Processing

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

3q3q


Resolution: 1.901→77 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 20.37
RfactorNum. reflection% reflection
Rfree0.2035 2573 5.08 %
Rwork0.1674 --
obs0.1692 50640 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.901→77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4026 0 38 410 4474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144160
X-RAY DIFFRACTIONf_angle_d1.3385638
X-RAY DIFFRACTIONf_dihedral_angle_d13.5111538
X-RAY DIFFRACTIONf_chiral_restr0.064618
X-RAY DIFFRACTIONf_plane_restr0.007742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.901-1.93760.37571400.30222631X-RAY DIFFRACTION99
1.9376-1.97710.25291380.25192612X-RAY DIFFRACTION100
1.9771-2.02010.29051480.22832623X-RAY DIFFRACTION100
2.0201-2.06710.23821370.21082616X-RAY DIFFRACTION100
2.0671-2.11880.22591420.19362649X-RAY DIFFRACTION100
2.1188-2.17610.23471610.17892610X-RAY DIFFRACTION100
2.1761-2.24010.21071420.17192641X-RAY DIFFRACTION100
2.2401-2.31250.20371270.16772647X-RAY DIFFRACTION100
2.3125-2.39510.20891460.16662640X-RAY DIFFRACTION100
2.3951-2.4910.19481570.15922632X-RAY DIFFRACTION100
2.491-2.60440.22381590.16212620X-RAY DIFFRACTION100
2.6044-2.74170.20741240.15442695X-RAY DIFFRACTION100
2.7417-2.91350.19431330.15152665X-RAY DIFFRACTION100
2.9135-3.13840.17251510.15212671X-RAY DIFFRACTION100
3.1384-3.45430.17231630.14062687X-RAY DIFFRACTION100
3.4543-3.95410.16571140.13642755X-RAY DIFFRACTION100
3.9541-4.98160.17431520.13812741X-RAY DIFFRACTION100
4.9816-77.06270.19511390.18142932X-RAY DIFFRACTION99
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)
10.5730.1608-0.1821.5249-0.22850.95240.0206-0.02710.00990.007-0.0101-0.0903-0.01140.0302-0.0140.08890.00480.01980.0930.00120.092416.99011.048936.2562
23.7949-1.87190.42476.0872-2.02244.6732-0.00520.43930.08-0.26380.07710.2393-0.17060.0864-0.08570.1529-0.0302-0.02990.16840.0480.13489.303417.854412.9315
32.13820.2310.60581.26970.95361.561-0.0410.0666-0.0506-0.15730.1086-0.1015-0.20210.0713-0.04840.1456-0.01630.0370.08540.01990.091124.013914.82425.8838
43.49341.6351-0.26776.8372.36911.6269-0.0346-0.1521-0.2661-0.38890.0204-0.5640.1010.28090.02510.23170.0080.08930.16030.04130.151329.50073.246413.4527
51.958-0.6174-1.51342.3275-0.74624.4802-0.11670.0014-0.1155-0.28270.0215-0.07890.1986-0.02680.1070.2082-0.02420.02750.0538-0.04390.101210.8072-18.213819.399
61.79282.11341.53333.36331.91162.0866-0.09250.2722-0.0557-0.32610.0962-0.1607-0.09460.1665-0.01810.18520.02150.0670.13140.00920.126922.8045-7.144717.5592
71.46710.96240.45081.17470.20930.418-0.05960.0323-0.0434-0.09330.0359-0.12920.01120.06110.01190.11960.01580.02950.1075-0.00090.103220.0516-4.176728.6081
80.7932-0.92410.80994.5329-2.02161.44280.04480.2090.0898-0.4249-0.01910.25290.055-0.0774-0.01630.19370.0349-0.03350.23390.04080.1449-9.26069.939816.3208
90.9067-0.77290.6981.36850.00581.6462-0.01340.03850.2601-0.1090.02510.2894-0.1296-0.2404-0.01290.15360.0465-0.00810.20750.05110.2322-13.174615.900223.8638
101.09860.11040.18770.7634-0.11070.73790.0462-0.02870.08290.0151-0.01970.0091-0.072-0.0238-0.02020.10930.00850.02470.08120.00550.08729.63317.885936.9055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 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 407 )
9X-RAY DIFFRACTION9chain 'A' and (resid 408 through 438 )
10X-RAY DIFFRACTION10chain 'A' and (resid 439 through 560 )

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