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- PDB-1qtj: CRYSTAL STRUCTURE OF LIMULUS POLYPHEMUS SAP -

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Basic information

Entry
Database: PDB / ID: 1qtj
TitleCRYSTAL STRUCTURE OF LIMULUS POLYPHEMUS SAP
ComponentsPROTEIN (SERUM AMYLOID P COMPONENT)
KeywordsSUGAR BINDING PROTEIN / PENTRAXIN FOLD / PHYSIOLOGICAL DOUBLY-STACKED OCTAMER / CYCLIC OCTAMER / INVERTEBRATE LECTIN
Biological speciesLimulus polyphemus (Atlantic horseshoe crab)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsShrive, A.K. / Metcalfe, A.M. / Cartwright, J.R. / Greenhough, T.J.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: C-reactive protein and SAP-like pentraxin are both present in Limulus polyphemus haemolymph: crystal structure of Limulus SAP.
Authors: Shrive, A.K. / Metcalfe, A.M. / Cartwright, J.R. / Greenhough, T.J.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: Three Dimensional Structure of Human C-reactive Protein
Authors: Shrive, A.K. / Cheetham, G.M.T. / Holden, D. / Myles, D.A.A. / Turnell, W.G. / Volanakis, J.E. / Pepys, M.B. / Bloomer, A.C. / Greenhough, T.J.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Preliminary Crystallographic Analysis of C-reactive Protein from Limulus Polyphemus
Authors: Myles, D.A.A. / Bailey, S. / Rule, S.A. / Jones, G.R. / Greenhough, T.J.
#3: Journal: J.Biol.Chem. / Year: 1996
Title: A Cytolytic Function for a Sialic Acid-Binding Lectin That is a Member of the Pentraxin Family of Proteins
Authors: Armstrong, P.B. / Swarnakar, S. / Srimal, S. / Misquith, S. / Hahn, E.A. / Aimes, R.T. / Quigley, J.P.
History
DepositionJun 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 16, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (SERUM AMYLOID P COMPONENT)
B: PROTEIN (SERUM AMYLOID P COMPONENT)


Theoretical massNumber of molelcules
Total (without water)36,9712
Polymers36,9712
Non-polymers00
Water00
1
A: PROTEIN (SERUM AMYLOID P COMPONENT)
B: PROTEIN (SERUM AMYLOID P COMPONENT)
x 8


Theoretical massNumber of molelcules
Total (without water)295,77216
Polymers295,77216
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)173.330, 173.330, 98.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2
DetailsThe biological assembly is a hexadecamer constructed of two cyclic octamers. This is generated by application of space group symmetry to the dimer ( protomers A and B) in the crystallographic asymmetric unit. THE BIOLOGICAL ASSEMBLY IS A HEXADECAMER CONSTRUCTED OF TWO CYCLIC OCTAMERS.

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Components

#1: Protein PROTEIN (SERUM AMYLOID P COMPONENT) / SAP


Mass: 18485.723 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Limulus polyphemus (Atlantic horseshoe crab)
Tissue: HAEMOLYMPH

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 %PEG60001reservoir
210 mM1reservoirCaCl2
3MES1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: CEA / Detector: FILM / Date: Jan 1, 1989
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 3→60 Å / Num. all: 13666 / Num. obs: 13666 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.117
Reflection shellResolution: 3→3.13 Å / Rmerge(I) obs: 0.284 / % possible all: 55.6
Reflection
*PLUS
Num. measured all: 47412
Reflection shell
*PLUS
% possible obs: 55.6 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
TFFCmodel building
Omodel building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
TFFCphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN C-REACTIVE PROTEIN PROTOMER (1GNH)

1gnh


Resolution: 3→15 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / σ(F): 0
Details: The polyalanine structure is a final fine-tune O fitting of the X-PLOR refined polyalanine chains A and B to the subsequently modified and averaged difference density. The NCS correlation in ...Details: The polyalanine structure is a final fine-tune O fitting of the X-PLOR refined polyalanine chains A and B to the subsequently modified and averaged difference density. The NCS correlation in DM between the two independent protomers was 0.938.
RfactorNum. reflection% reflection
Rfree0.401 665 5 %
Rwork0.397 --
obs-13429 87 %
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 0 0 2170
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDWeight position
11PROTOMER CHAIN A. GROUP 1 ALL MAIN CHAIN FOR CHAINS A AND B. GROUP 2 ALL SIDE CHAINS FOR CHAINS A AND B. NCS RESTRAINTS (X-PLOR).X-RAY DIFFRACTION500
22X-RAY DIFFRACTION300
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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