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- PDB-3lxq: The Crystal Structure of a Protein in the Alkaline Phosphatase Su... -

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Basic information

Entry
Database: PDB / ID: 3lxq
TitleThe Crystal Structure of a Protein in the Alkaline Phosphatase Superfamily from Vibrio parahaemolyticus to 1.95A
ComponentsUncharacterized protein VP1736
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Alkaline / phosphatase / MdoB / sulfatase / Vibrio / parahaemolyticus / PSI / MCSG / Midwest Center for Structural Genomics / Protein Structure Initiative
Function / homology
Function and homology information


sulfuric ester hydrolase activity / membrane => GO:0016020 / metal ion binding / plasma membrane
Similarity search - Function
Arylsulfatase, C-terminal domain - #80 / Lipoteichoic acid synthase-like / Arylsulfatase, C-terminal domain / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sulfatase domain-containing protein
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsStein, A.J. / Weger, A. / Duggan, E. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of a Protein in the Alkaline Phosphatase Superfamily from Vibrio parahaemolyticus to 1.95A
Authors: Stein, A.J. / Weger, A. / Duggan, E. / Clancy, S. / Joachimiak, A.
History
DepositionFeb 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein VP1736
B: Uncharacterized protein VP1736
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0544
Polymers102,9832
Non-polymers712
Water4,828268
1
A: Uncharacterized protein VP1736
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5272
Polymers51,4911
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein VP1736
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5272
Polymers51,4911
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.603, 164.521, 50.929
Angle α, β, γ (deg.)90.000, 109.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein VP1736


Mass: 51491.371 Da / Num. of mol.: 2 / Fragment: sequence database residues 200-649
Source method: isolated from a genetically manipulated source
Details: pMCSG7 / Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: VP1736 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87NY2
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 1.93 Å3/Da / Density % sol: 36.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 8000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 55351 / % possible obs: 98.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.105 / Χ2: 1.939 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.95-2.023.10.48154521.01698.1
2.02-2.13.10.37754781.02198.2
2.1-2.23.10.28854691.05498.2
2.2-2.313.10.2255381.13698.6
2.31-2.463.10.18555231.26599.1
2.46-2.653.10.14955541.47799.1
2.65-2.913.10.11955791.8199.9
2.91-3.333.10.09755602.45699.7
3.33-4.23.10.08156083.10199.8
4.2-503.10.08455905.02298.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
Cootmodel building
RefinementResolution: 1.95→40.99 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 11.36 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2813 5.1 %RANDOM
Rwork0.198 ---
obs0.2 55308 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.989 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6402 0 2 268 6672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226561
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.9528908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8795821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20824.7317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.288151052
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5241530
X-RAY DIFFRACTIONr_chiral_restr0.0890.2959
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215110
X-RAY DIFFRACTIONr_mcbond_it0.451.54078
X-RAY DIFFRACTIONr_mcangle_it0.76126556
X-RAY DIFFRACTIONr_scbond_it1.63932483
X-RAY DIFFRACTIONr_scangle_it2.2354.52349
LS refinement shellResolution: 1.949→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 179 -
Rwork0.27 3799 -
all-3978 -
obs--96.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
122.398612.0834-6.174413.8955-1.81862.2279-0.54551.6895-0.3508-0.75730.847-0.873-0.3674-0.4329-0.30151.0053-0.12550.01060.46970.00150.5735-5.780352.2751-31.9598
26.033-3.76020.79458.3513-3.51262.1560.0370.55130.3182-1.10480.1599-0.14370.26640.0973-0.1970.4863-0.15410.09320.31640.00760.32224.735161.9824-22.8999
31.6480.52680.78885.169-0.21622.92890.07840.2008-0.06670.05610.0329-1.0118-0.08860.5428-0.11130.2435-0.0098-0.05690.2512-0.07080.422512.471750.9445-10.772
45.9891-2.19461.40863.64131.67882.06520.1857-0.44810.49440.8493-0.2812-0.09840.633-0.40640.09551.0563-0.17640.08530.4720.11370.3514-5.754242.41665.9492
517.7187-0.33019.06763.29710.06924.69080.224-0.9196-0.40550.72080.139-0.27690.1537-0.5234-0.3630.561-0.02130.00210.27140.13690.42330.8351.75342.2815
63.23711.3115-0.75163.8859-0.95645.02170.08510.1511-0.30580.05860.2372-0.1480.1019-0.0291-0.32230.0894-0.0154-0.0540.1743-0.03120.28770.93243.6977-15.1269
75.887-0.24020.71195.52930.66111.80870.15510.5642-0.3258-0.67270.1152-0.68550.31710.1277-0.27030.2576-0.04970.06050.2666-0.07360.37167.645841.5725-22.3351
80.0635-0.02660.42462.34160.61473.19520.09310.04480.01250.04810.228-1.30920.64090.2573-0.32110.30450.0678-0.13420.3133-0.12570.83313.26634.6762-13.5111
91.19691.0718-2.56978.4206-5.43927.4865-0.0519-0.2345-0.0722-0.19250.0221-1.00150.84190.40630.02980.68110.0519-0.42620.2451-0.03930.780312.266926.2612-6.6513
102.74481.11990.05932.23840.0092.65530.24130.1468-0.25440.54320.0299-0.54270.51250.3154-0.27120.50280.0066-0.25270.23520.00380.46778.982531.3594-1.9201
118.7209-0.74134.46858.2252-0.17894.19170.3045-0.2647-0.39740.8948-0.0810.13980.5643-0.3099-0.22350.9216-0.20660.05520.34650.08960.4487-9.017427.18676.5004
127.86322.65021.34031.13681.09762.94840.3457-0.26380.21320.534-0.1139-0.0310.68880.0271-0.23180.9551-0.1067-0.250.2360.07140.38453.916334.91766.9829
138.13030.7163.42684.10430.43294.49070.5446-0.0501-0.23460.537-0.14070.03110.5569-0.2786-0.40390.2913-0.03360.00280.17440.03290.2482-1.596143.0627-5.995
140.49030.5876-0.87971.7702-0.8531.62340.2251-0.10320.01250.992-0.0824-0.4452-0.28760.1682-0.14260.6436-0.0674-0.20550.242-0.03630.40345.866752.0558-2.4148
153.12712.05481.55194.16320.46592.1480.00690.126-0.11030.0640.10740.0097-0.0954-0.1171-0.11430.2206-0.01110.0150.2730.02490.25290.926255.7132-13.5126
165.2824-1.10481.08626.6781-2.81741.26560.05030.18070.17160.37530.41411.2793-0.1582-0.1539-0.46440.23170.0713-0.01940.34930.1010.5314-12.4156.2932-17.8479
177.20532.53273.29453.83842.91462.56150.142-0.83530.409-0.408-1.30032.018-0.1777-0.99421.15840.54660.206-0.17971.0216-0.19221.5132-16.731256.3049-17.3586
182.06111.22431.82222.1454-27.605246.4528-0.2426-0.83910.6878-0.43780.67852.3342-0.5985-1.8713-0.43590.43340.27470.00130.63890.10591.0288-17.125559.3141-11.8732
194.72390.8976-2.48114.98313.26374.2353-0.20950.51190.5687-0.89890.31770.3915-0.5944-0.1938-0.10820.46440.0096-0.08110.35970.1140.2616-4.839758.0382-23.8182
203.8585-1.9088-3.18887.714-1.20024.6616-0.14970.34080.0309-1.0660.2464-0.2240.4160.1981-0.09670.4657-0.16580.11830.5405-0.10180.3478.51648.733-28.2724
211.3173-2.4376-2.65294.59465.11275.86940.2115-0.11190.4812-0.18360.4202-0.78590.04810.5801-0.63170.46570.13450.16160.61960.10750.653110.2625-3.8075-3.7333
221.79650.1639-0.28613.3022-0.61494.4625-0.17350.0526-0.4096-0.3685-0.1521-0.4010.56790.7290.32560.27990.1680.09150.41410.07130.27336.6543-11.0782-18.9136
234.8563-1.81565.62742.0771-1.53079.6714-0.07380.33060.0793-0.3128-0.0055-0.21830.17610.64450.07940.25970.07860.12310.25510.00230.21751.478-8.0553-28.5442
241.95-0.7414-1.06131.42550.28654.1631-0.09910.0566-0.05030.0388-0.07950.217-0.1259-0.25780.17860.0968-0.0117-0.0140.19580.00130.1779-16.29458.4202-23.8
2512.169-5.45517.40182.5095-8.508133.6497-0.1003-0.5027-0.01950.12310.25180.0794-1.0642-0.784-0.15150.1312-0.08840.00710.2801-0.00380.5002-19.73540.7975-25.4447
268.41164.7178-1.91255.8206-2.62183.0277-0.24320.0139-0.1471-0.13230.06630.0715-0.01790.12940.1770.01570.00790.02070.22430.0190.1644-9.07655.3558-13.063
272.6569-2.0211-0.38084.11142.23784.9723-0.0372-0.02040.15660.0946-0.1174-0.2468-0.21340.55060.15470.0702-0.05860.01970.28460.04360.17771.81357.3817-15.5953
281.73730.61380.51550.9511.60936.8936-0.20190.06070.0468-0.14550.1241-0.3008-0.48260.86210.07780.0836-0.07220.01660.42110.0530.29838.62218.9189-21.3148
293.097-2.8791-1.63676.30323.57476.08750.04020.03830.2974-0.09330.0558-0.6797-0.21530.5428-0.0960.1088-0.0930.03690.31170.05750.16561.26512.823-31.7523
300.5391-0.45061.33651.1314-0.84623.5133-0.09770.06820.1006-0.0693-0.08540.0322-0.36010.30280.18310.2406-0.12750.010.35450.00810.29043.605417.8524-26.5448
311.7827-1.1304-0.97582.72670.90212.38710.01620.09670.2076-0.2297-0.0636-0.0617-0.66430.11990.04750.2532-0.0391-0.04010.22990.0270.1833-9.370721.179-29.9463
324.1377-2.84932.33564.3766-3.3919.7087-0.1023-0.09770.58220.12580.14070.279-0.6959-0.1443-0.03840.38890.1362-0.00330.3022-0.0420.3374-24.35125.1234-16.4531
330.8047-0.2858-0.43811.8234-0.31493.7921-0.02850.110.1021-0.1681-0.07840.1197-0.2952-0.11890.10680.0808-0.0072-0.0170.2112-0.00960.199-16.081913.1519-27.544
341.5263-0.211.1222.7014-0.3577.8683-0.0903-0.01930.01050.0466-0.06830.1481-0.1778-0.31070.15870.0184-0.01050.03710.194-0.00770.1676-13.37754.7213-15.5205
350.0359-0.10690.13770.3338-0.28642.68990.0270.03530.0069-0.0938-0.09790.0130.3550.15730.07090.15810.0020.04070.2555-0.00330.2153-6.5639-4.1841-24.4324
368.02164.16461.43711.44344.48936.77620.11990.1199-0.32020.0931-0.1198-0.23620.53720.132800.23830.05040.02820.24460.04460.1487-8.8191-9.1154-13.0633
372.66580.41810.7653.0534-1.38296.23550.074-0.2223-0.10840.5655-0.1544-0.25860.09950.40540.08040.15720.02490.01170.28370.01110.17-3.7309-0.9911-2.2239
3815.0546-12.1058.528210.2144-8.6111.2782-0.2158-0.2883-0.14560.16470.25080.0914-0.1185-0.4103-0.0350.0941-0.03760.12970.33450.01550.1984-16.4923-2.9365-2.3037
3914.4742-3.1898-1.67146.86130.69495.3372-0.0921-0.4499-0.43440.1342-0.0660.1010.28860.09350.15810.2788-0.00950.00990.28750.05840.1127-7.1604-10.09212.1189
402.14352.3883-2.75825.4874-2.24115.16190.0442-0.12-0.18660.101-0.1832-0.49610.06910.87260.13910.03730.05740.0140.45930.05050.24348.6384-1.8187-12.1231
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A239 - 249
2X-RAY DIFFRACTION2A250 - 264
3X-RAY DIFFRACTION3A265 - 297
4X-RAY DIFFRACTION4A298 - 316
5X-RAY DIFFRACTION5A317 - 325
6X-RAY DIFFRACTION6A326 - 344
7X-RAY DIFFRACTION7A345 - 367
8X-RAY DIFFRACTION8A368 - 394
9X-RAY DIFFRACTION9A395 - 412
10X-RAY DIFFRACTION10A413 - 455
11X-RAY DIFFRACTION11A456 - 470
12X-RAY DIFFRACTION12A471 - 492
13X-RAY DIFFRACTION13A493 - 520
14X-RAY DIFFRACTION14A521 - 554
15X-RAY DIFFRACTION15A555 - 589
16X-RAY DIFFRACTION16A590 - 599
17X-RAY DIFFRACTION17A600 - 608
18X-RAY DIFFRACTION18A609 - 621
19X-RAY DIFFRACTION19A622 - 634
20X-RAY DIFFRACTION20A635 - 647
21X-RAY DIFFRACTION21B239 - 252
22X-RAY DIFFRACTION22B253 - 270
23X-RAY DIFFRACTION23B271 - 280
24X-RAY DIFFRACTION24B281 - 315
25X-RAY DIFFRACTION25B316 - 322
26X-RAY DIFFRACTION26B323 - 332
27X-RAY DIFFRACTION27B333 - 349
28X-RAY DIFFRACTION28B350 - 366
29X-RAY DIFFRACTION29B367 - 384
30X-RAY DIFFRACTION30B385 - 403
31X-RAY DIFFRACTION31B404 - 456
32X-RAY DIFFRACTION32B457 - 470
33X-RAY DIFFRACTION33B471 - 509
34X-RAY DIFFRACTION34B510 - 532
35X-RAY DIFFRACTION35B533 - 569
36X-RAY DIFFRACTION36B570 - 579
37X-RAY DIFFRACTION37B580 - 603
38X-RAY DIFFRACTION38B604 - 613
39X-RAY DIFFRACTION39B614 - 624
40X-RAY DIFFRACTION40B625 - 645

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