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- PDB-4jod: Crystal structure of human lysophosphatidic acid phosphatase type... -

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Basic information

Entry
Database: PDB / ID: 4jod
TitleCrystal structure of human lysophosphatidic acid phosphatase type 6 complexed with Tris
ComponentsLysophosphatidic acid phosphatase type 6
KeywordsHYDROLASE / Rossmann Fold / mitochondria
Function / homology
Function and homology information


lysobisphosphatidic acid metabolic process / phosphatidic acid biosynthetic process / Synthesis of PA / acid phosphatase / lysophosphatidic acid phosphatase activity / acid phosphatase activity / hematopoietic progenitor cell differentiation / phospholipid metabolic process / dephosphorylation / mitochondrial matrix ...lysobisphosphatidic acid metabolic process / phosphatidic acid biosynthetic process / Synthesis of PA / acid phosphatase / lysophosphatidic acid phosphatase activity / acid phosphatase activity / hematopoietic progenitor cell differentiation / phospholipid metabolic process / dephosphorylation / mitochondrial matrix / mitochondrion / cytoplasm
Similarity search - Function
Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Phosphoglycerate mutase-like / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Lysophosphatidic acid phosphatase type 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.21 Å
AuthorsLi, J.
CitationJournal: Protein Cell / Year: 2013
Title: Crystal structures and biochemical studies of human lysophosphatidic acid phosphatase type 6.
Authors: Li, J. / Dong, Y. / Lu, X. / Wang, L. / Peng, W. / Zhang, X.C. / Rao, Z.
History
DepositionMar 18, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Other
Revision 1.2Aug 14, 2013Group: Database references
Revision 1.3Nov 15, 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: Lysophosphatidic acid phosphatase type 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4862
Polymers45,3641
Non-polymers1221
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.045, 90.708, 95.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysophosphatidic acid phosphatase type 6 / Acid phosphatase 6 / lysophosphatidic / Acid phosphatase-like protein 1 / PACPL1


Mass: 45363.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACP6 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NPH0, acid phosphatase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMET 316 CORRESPONDS TO VARIANT RS6593795.

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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: 2.66 Å3/Da / Density % sol: 54 % / Mosaicity: 0.739 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.02M citric acid, 0.08M bis-tris propane, 16% PEG3350, pH 8.0, vapor diffusion, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 7 % / Av σ(I) over netI: 16.91 / Number: 166427 / Rmerge(I) obs: 0.095 / Χ2: 1.04 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 23688 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.745099.210.0661.0926
3.764.7499.810.061.0866.6
3.293.7699.910.0711.0636.9
2.993.2999.910.0931.0047.1
2.772.9910010.1221.037.2
2.612.7710010.1581.0587.3
2.482.6110010.2091.0637.3
2.372.4810010.2731.0717.3
2.282.3710010.3530.9867.3
2.22.2810010.4570.9887.3
ReflectionResolution: 2.2→50 Å / Num. obs: 23688 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.095 / Χ2: 1.043 / Net I/σ(I): 16.907
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.287.30.45723260.9881100
2.28-2.377.30.35323270.9861100
2.37-2.487.30.27323341.0711100
2.48-2.617.30.20923301.0631100
2.61-2.777.30.15823511.0581100
2.77-2.997.20.12223361.031100
2.99-3.297.10.09323911.004199.9
3.29-3.766.90.07123691.063199.9
3.76-4.746.60.0623971.086199.8
4.74-5060.06625271.092199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.21→46.39 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8817 / SU ML: 0.18 / σ(F): 0 / Phase error: 18.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1172 5.11 %RANDOM
Rwork0.1688 21746 --
obs0.1704 22918 96.41 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.643 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 141.59 Å2 / Biso mean: 39.7346 Å2 / Biso min: 13.45 Å2
Baniso -1Baniso -2Baniso -3
1-9.959 Å2-0 Å20 Å2
2---11.1465 Å20 Å2
3---1.1875 Å2
Refinement stepCycle: LAST / Resolution: 2.21→46.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 8 136 3190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063132
X-RAY DIFFRACTIONf_angle_d0.9964245
X-RAY DIFFRACTIONf_chiral_restr0.075462
X-RAY DIFFRACTIONf_plane_restr0.006549
X-RAY DIFFRACTIONf_dihedral_angle_d14.5771193
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2103-2.31090.21691230.18652392251587
2.3109-2.43270.23661350.18862570270593
2.4327-2.58510.25791810.19282634281596
2.5851-2.78470.21661580.18212712287098
2.7847-3.06490.18161350.17672779291499
3.0649-3.50820.20771550.164528212976100
3.5082-4.41950.18421500.151228513001100
4.4195-46.40030.18191350.16532987312299
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)
10.6909-0.50210.65881.05640.1441.11570.0090.12230.1637-0.0153-0.1142-0.40160.01710.2022-0.04410.1007-0.00110.04530.21590.07640.212722.472121.634435.9005
20.174-0.21350.09710.6701-0.23380.81740.02660.03960.1411-0.2275-0.14450.0917-0.12890.0104-0.00970.20990.0206-0.06290.17050.01460.20533.637532.11129.643
30.1941-0.06050.1560.25690.02010.15710.15880.1498-0.2354-0.5041-0.07610.16560.08970.11180.00590.25890.0420.01050.2467-0.02580.212414.048810.657628.4801
40.3963-0.16560.33350.3450.08290.4510.2063-0.0208-0.1039-0.2329-0.12070.10520.1551-0.15970.30650.3053-0.0502-0.0530.1773-0.0120.17824.667710.298831.1327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 42:197)A42 - 197
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 198:315)A198 - 315
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 316:344)A316 - 344
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 345:419)A345 - 419

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