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- PDB-3q3q: Crystal Structure of SPAP: an novel alkaline phosphatase from bac... -

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Basic information

Entry
Database: PDB / ID: 3q3q
TitleCrystal Structure of SPAP: an novel alkaline phosphatase from bacterium Sphingomonas sp. strain BSAR-1
ComponentsAlkaline phosphatase
KeywordsHYDROLASE / Alkaline phosphatase
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
methyl dihydrogen phosphate / Alkaline phosphatase PhoK
Similarity search - Component
Biological speciesSphingomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.953 Å
AuthorsBihani, S.C. / Hosur, M.V.
CitationJournal: Plos One / Year: 2011
Title: X-ray structure reveals a new class and provides insight into evolution of alkaline phosphatases
Authors: Bihani, S.C. / Das, A. / Nilgiriwala, K.S. / Prashar, V. / Pirocchi, M. / Apte, S.K. / Ferrer, J.-L. / Hosur, M.V.
History
DepositionDec 22, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,62110
Polymers60,8781
Non-polymers7439
Water5,008278
1
A: Alkaline phosphatase
hetero molecules

A: Alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,24220
Polymers121,7562
Non-polymers1,48718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4140 Å2
ΔGint-13 kcal/mol
Surface area36480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.370, 87.370, 168.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-793-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alkaline phosphatase /


Mass: 60877.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. (bacteria) / Strain: BSAR-1 / Gene: phoK / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / References: UniProt: A1YYW7, alkaline phosphatase

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Non-polymers , 5 types, 287 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-KOP / methyl dihydrogen phosphate


Mass: 112.022 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5O4P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsKOP IS AN ORGANIC MONOPHOSPHATE, R-OPO3, WHERE R IS NOT FIXED. AT PRESENT, METHYL GROUP IS PUTTING ...KOP IS AN ORGANIC MONOPHOSPHATE, R-OPO3, WHERE R IS NOT FIXED. AT PRESENT, METHYL GROUP IS PUTTING FOR R FOR CONVENIENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M Ammonium Sulfate, 10% Dioxane, 100mM MES Buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM30A10.980159
SYNCHROTRONESRF BM30A20.976261, 0.980159, 0.980337
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMar 17, 2009
ADSC QUANTUM 315r2CCDMar 17, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9801591
20.9762611
30.9803371
ReflectionResolution: 1.95→49.785 Å / Num. obs: 87058 / Biso Wilson estimate: 31.39 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.953→49.785 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8978 / SU ML: 0.25 / σ(F): 1.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1863 4420 5.08 %
Rwork0.1553 --
obs0.1569 87053 96.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.003 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 146.98 Å2 / Biso mean: 42.3213 Å2 / Biso min: 14.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.0129 Å20 Å2-0 Å2
2--0.0129 Å2-0 Å2
3----0.0259 Å2
Refinement stepCycle: LAST / Resolution: 1.953→49.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 39 278 4317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074148
X-RAY DIFFRACTIONf_angle_d1.0195625
X-RAY DIFFRACTIONf_chiral_restr0.07615
X-RAY DIFFRACTIONf_plane_restr0.004741
X-RAY DIFFRACTIONf_dihedral_angle_d16.2731524
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9531-2.02290.25154320.22458005843794
2.0229-2.10390.2384160.20218456887298
2.1039-2.19960.20594310.17418423885498
2.1996-2.31560.19664480.16218349879798
2.3156-2.46070.20374370.15328378881598
2.4607-2.65060.21724520.16018341879397
2.6506-2.91740.19774480.14778307875597
2.9174-3.33940.18774430.15148242868596
3.3394-4.2070.1634660.13688162862896
4.207-49.80150.15474470.14277970841793
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)
10.9946-0.91410.31531.12580.59442.846-0.7802-0.18960.2091.0490.6138-0.0669-1.20130.46690.25680.89570.0611-0.19710.47720.00130.4007-0.901832.54387.9542
20.4574-0.59620.66260.847-1.0781.4641-0.08830.11280.04410.10540.05080.1061-0.0925-0.11430.00970.1364-0.0511-0.03380.22240.05810.199-1.407615.6973-6.8906
33.76120.98691.05862.07762.36362.82310.38060.535-0.423-0.6058-0.07190.0422-0.1775-0.4865-0.21090.3083-0.0536-0.19320.51720.03940.3698-17.8119.8146-30.0758
41.1608-0.72870.74630.5934-0.78091.1215-0.02410.41610.12570.01290.10720.1327-0.0863-0.3433-0.0950.1591-0.028-0.030.3920.14080.2828-12.129124.9377-19.1281
51.9668-1.33621.50775.0935-0.82813.15760.19910.67541.02080.2091-0.5761-1.201-0.32730.80410.77010.1554-0.1932-0.17190.58260.44440.46753.516232.2751-29.3903
61.54310.0723-0.55111.2433-1.49942.44030.08050.62590.1168-0.2176-0.2388-0.08080.25460.46860.16980.21830.0411-0.00020.68860.14080.238616.301912.3177-23.9418
71.2176-0.87630.73940.7393-0.72771.50820.0060.44350.17390.0478-0.1489-0.1761-0.05460.19880.16090.1561-0.0831-0.04480.29740.10330.19984.760618.8171-14.3532
82.69530.62832.4981.94090.48243.62480.560.6179-0.7166-0.49410.10090.89390.626-0.3647-0.50890.6089-0.1656-0.46610.4683-0.11380.5838-13.6951-9.5081-27.5395
92.6064-0.59682.05450.1362-0.47051.61870.5330.4668-1.5617-0.88660.51430.21040.6464-0.1534-1.11140.659-0.3338-0.55430.53250.00871.1763-22.0333-15.2684-23.0468
101.8979-0.10261.13871.151-1.04431.5190.3558-0.0158-0.4703-0.20360.13920.48740.5485-0.3945-0.39120.2945-0.188-0.18690.3270.08050.4443-11.5138-4.0724-11.1543
113.5337-1.71312.65463.8915-3.97354.36550.22850.8813-0.0733-0.6594-0.56650.08870.97271.73540.07430.68750.1264-0.16380.7179-0.15330.4046.8966-3.3031-29.8266
121.0966-0.42970.78791.1304-1.0321.9902-0.1208-0.0393-0.02690.33950.21110.169-0.1877-0.3545-0.0980.1996-0.00730.00770.26030.07620.2287-5.845416.5631-0.1214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 31:36)A31 - 36
2X-RAY DIFFRACTION2(chain A and resid 37:110)A37 - 110
3X-RAY DIFFRACTION3(chain A and resid 111:141)A111 - 141
4X-RAY DIFFRACTION4(chain A and resid 142:201)A142 - 201
5X-RAY DIFFRACTION5(chain A and resid 202:221)A202 - 221
6X-RAY DIFFRACTION6(chain A and resid 222:261)A222 - 261
7X-RAY DIFFRACTION7(chain A and resid 262:367)A262 - 367
8X-RAY DIFFRACTION8(chain A and resid 368:404)A368 - 404
9X-RAY DIFFRACTION9(chain A and resid 405:420)A405 - 420
10X-RAY DIFFRACTION10(chain A and resid 421:480)A421 - 480
11X-RAY DIFFRACTION11(chain A and resid 481:486)A481 - 486
12X-RAY DIFFRACTION12(chain A and resid 487:556)A487 - 556

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