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

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Basic information

Entry
Database: PDB / ID: 4job
TitleCrystal structure of human lysophosphatidic acid phosphatase type 6 complexed with L-(+)-tartrate
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 / phospholipid metabolic process / hematopoietic progenitor cell differentiation / dephosphorylation / mitochondrial matrix ...lysobisphosphatidic acid metabolic process / phosphatidic acid biosynthetic process / Synthesis of PA / acid phosphatase / lysophosphatidic acid phosphatase activity / acid phosphatase activity / phospholipid metabolic process / hematopoietic progenitor cell differentiation / 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
L(+)-TARTARIC ACID / Lysophosphatidic acid phosphatase type 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.171 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 1.1Aug 14, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysophosphatidic acid phosphatase type 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5142
Polymers45,3641
Non-polymers1501
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.319, 91.028, 104.959
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.5 Å3/Da / Density % sol: 51 % / Mosaicity: 0.833 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M sodium tartrate dibasic dihydrate, 20% PEG3350, pH 7.5, 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: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 23126 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 37.2 Å2 / Rmerge(I) obs: 0.085 / Χ2: 1.053 / Net I/σ(I): 19.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.17-2.255.80.45722651.091199.3
2.25-2.346.80.44722831.0851100
2.34-2.447.10.30922771.0721100
2.44-2.577.10.2422581.0761100
2.57-2.737.10.18923051.0591100
2.73-2.9570.14223101.0941100
2.95-3.246.80.10623031.0151100
3.24-3.716.50.07823290.9971100
3.71-4.676.20.06323510.979199.9
4.67-5060.05624971.06199.5

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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
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.171→45.514 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.7742 / SU ML: 0.29 / σ(F): 0 / Phase error: 28.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 1888 8.65 %RANDOM
Rwork0.2005 ---
obs0.2048 21832 94.24 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.805 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso max: 148 Å2 / Biso mean: 52.5269 Å2 / Biso min: 18.58 Å2
Baniso -1Baniso -2Baniso -3
1-10.9818 Å2-0 Å20 Å2
2---17.1139 Å20 Å2
3---6.1321 Å2
Refinement stepCycle: LAST / Resolution: 2.171→45.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2978 0 10 75 3063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093183
X-RAY DIFFRACTIONf_angle_d0.9114158
X-RAY DIFFRACTIONf_chiral_restr0.066455
X-RAY DIFFRACTIONf_plane_restr0.004537
X-RAY DIFFRACTIONf_dihedral_angle_d14.8571175
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1711-2.22980.43041040.34861180128473
2.2298-2.29540.40591250.3591289141482
2.2954-2.36950.30511390.2361462160191
2.3695-2.45410.28681480.22611513166195
2.4541-2.55240.25281440.21541509165395
2.5524-2.66860.26831450.20661558170397
2.6686-2.80920.3261520.22561572172497
2.8092-2.98520.29441510.23551595174698
2.9852-3.21560.28751510.21681593174499
3.2156-3.53910.22421520.20031614176699
3.5391-4.0510.2071550.16561651180699
4.051-5.10270.18561550.148216531808100
5.1027-45.5240.24341670.200917551922100
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)
10.1513-0.0350.07150.2765-0.06160.06540.11770.1436-0.1348-0.7623-0.09230.06420.1531-0.07330.00420.24790.00660.00730.36450.02450.3175-14.9579-3.54249.7573
20.27410.20040.2280.17360.19740.23530.0694-0.3267-0.88260.4509-0.1618-0.32530.6293-0.08-0.07120.55010.04490.01670.19030.08350.7396-4.9511-40.44889.2794
30.37990.33160.13342.7349-1.26431.00180.0364-0.1407-0.3902-0.3997-0.5615-1.30010.52310.4488-0.26150.2434-0.1333-0.22520.47540.13990.55986.1638-20.753915.7064
40.5292-0.0308-0.24932.62660.24140.18410.0866-0.0186-0.4154-0.5538-0.01890.16870.0964-0.00890.02810.15930.0110.0090.2790.03490.269-3.1154-26.11817.5104
50.25850.12390.04270.36140.23730.14830.0972-0.043-0.0594-0.0391-0.2317-0.4373-0.08230.3233-0.00120.2506-0.01240.02340.3386-0.00220.3486-0.764-12.737110.609
60.1803-0.52850.1481.51680.311.01890.0719-0.1136-0.04560.4101-0.09360.04730.1866-0.00050.00020.3649-0.0394-0.10070.28850.05490.2625-13.2016-29.354523.5627
70.33330.31980.37720.25820.42140.4478-0.04180.023-0.0119-0.17530.06930.10530.2475-0.0061-0.00050.4056-0.0324-0.02540.21610.00430.3114-19.2373-38.238913.1779
80.1104-0.06170.01330.13490.0425-0.00780.02750.05930.06530.6390.17350.2476-0.0192-0.00340.0010.3786-0.0236-0.01460.3303-0.00130.3071-15.4975-11.331126.4678
90.2479-0.23820.03680.2657-0.20960.4166-0.0066-0.30780.1284-0.01040.0192-0.05580.04970.0839-0.00020.2803-0.0146-0.00880.3280.00120.28-13.3798-16.607716.6609
100.0479-0.1668-0.07920.2493-0.11380.25430.01040.3230.0587-0.45110.09690.3338-0.2414-0.09-0.0020.36450.0093-0.00160.32540.01410.353-20.4112-4.689912.0548
111.08530.0483-0.02630.1032-0.16050.3770.1553-0.11850.16210.6893-0.2072-0.19-0.0928-0.17550.00670.5465-0.046-0.01980.3066-0.03160.2719-18.1941-12.056931.4969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 42:58)A42 - 58
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 59:81)A59 - 81
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 82:105)A82 - 105
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 106:143)A106 - 143
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 144:181)A144 - 181
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 182:239)A182 - 239
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 240:293)A240 - 293
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 294:316)A294 - 316
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 317:357)A317 - 357
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 358:394)A358 - 394
11X-RAY DIFFRACTION11CHAIN A AND (RESSEQ 395:419)A395 - 419

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