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- PDB-2hsj: The structure of a putative platelet activating factor from Strep... -

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Basic information

Entry
Database: PDB / ID: 2hsj
TitleThe structure of a putative platelet activating factor from Streptococcus pneumonia.
ComponentsPutative platelet activating factor
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / platelet activating factor / Streptococcus pneumonia / structral genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative platelet activating factor / Putative platelet activating factor
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsCuff, M.E. / Mulligan, R. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of a putative platelet activating factor from Streptococcus pneumonia.
Authors: Cuff, M.E. / Mulligan, R. / Abdullah, J. / Joachimiak, A.
History
DepositionJul 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS UNKNOWN, BUT AUTHORS SUGGEST THE DIMERS FORMED BY CHAINS A+D AND B+C MAY BE RELEVANT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative platelet activating factor
B: Putative platelet activating factor
C: Putative platelet activating factor
D: Putative platelet activating factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,01720
Polymers98,0184
Non-polymers99916
Water22,8071266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8690 Å2
ΔGint-71 kcal/mol
Surface area37410 Å2
MethodPISA
2
A: Putative platelet activating factor
D: Putative platelet activating factor
hetero molecules

B: Putative platelet activating factor
C: Putative platelet activating factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,01720
Polymers98,0184
Non-polymers99916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area10320 Å2
ΔGint-84 kcal/mol
Surface area35680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.032, 120.063, 84.743
Angle α, β, γ (deg.)90.00, 99.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative platelet activating factor


Mass: 24504.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP1450 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q97PY9, UniProt: A0A0H2UQU7*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1266 / 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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl2, 0.1M Tris, 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926, 0.97943
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.979431
ReflectionResolution: 1.5→40.46 Å / Num. all: 128174 / Num. obs: 128174 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.5→1.55 Å / % possible all: 88.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
autoSHARPphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.5→40.46 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.47 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.078
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19311 6428 5 %RANDOM
Rwork0.15996 ---
obs0.16161 121745 99.44 %-
all-121745 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.539 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.07 Å2
2---0.24 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6843 0 61 1266 8170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227285
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9699916
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3815900
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.35425.69355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.194151289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7311524
X-RAY DIFFRACTIONr_chiral_restr0.0920.21109
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025535
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.23630
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.25123
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2955
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0030.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.2175
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.279
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0210.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9291.54510
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42727123
X-RAY DIFFRACTIONr_scbond_it2.54133175
X-RAY DIFFRACTIONr_scangle_it3.7914.52793
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 453 -
Rwork0.237 8438 -
obs--93.32 %
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)
10.80330.202-0.09281.22120.3510.67330.0071-0.001-0.1075-0.0204-0.0161-0.06990.0188-0.00670.0089-0.04750.00510.0094-0.03880.0078-0.031210.929674.333110.946
20.76260.06940.02370.53390.10420.2227-0.0007-0.01330.09340.0527-0.011-0.01610.007-0.00850.0117-0.0207-0.0129-0.0054-0.02490.006-0.02761.803102.874551.7549
30.56220.1377-0.03450.5242-0.08930.21490.0135-0.0072-0.0450.0264-0.01530.00370.00220.02910.0018-0.0166-0.00990.0049-0.01620.0002-0.0356-7.89475.413951.3625
40.52680.05410.13321.12740.1330.7659-0.02190.03390.017-0.17770.01270.0124-0.12140.02830.00920.01060.0031-0.0038-0.0432-0.0101-0.0578.9073103.607411.1737
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2114 - 214
2X-RAY DIFFRACTION2BB0 - 2113 - 214
3X-RAY DIFFRACTION3CC0 - 2113 - 214
4X-RAY DIFFRACTION4DD-1 - 2112 - 214

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