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- PDB-1lgn: DECAMERIC DAMP COMPLEX OF HUMAN SERUM AMYLOID P COMPONENT -

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Basic information

Entry
Database: PDB / ID: 1lgn
TitleDECAMERIC DAMP COMPLEX OF HUMAN SERUM AMYLOID P COMPONENT
ComponentsSERUM AMYLOID P COMPONENT
KeywordsSERUM PROTEIN / AMYLOIDOSIS / DRUG DESIGN / NUCLEOTIDE
Function / homology
Function and homology information


negative regulation by host of viral glycoprotein metabolic process / negative regulation of glycoprotein metabolic process / complement component C1q complex binding / negative regulation of viral process / negative regulation of wound healing / negative regulation of monocyte differentiation / host-mediated suppression of symbiont invasion / virion binding / negative regulation of acute inflammatory response / chaperone-mediated protein complex assembly ...negative regulation by host of viral glycoprotein metabolic process / negative regulation of glycoprotein metabolic process / complement component C1q complex binding / negative regulation of viral process / negative regulation of wound healing / negative regulation of monocyte differentiation / host-mediated suppression of symbiont invasion / virion binding / negative regulation of acute inflammatory response / chaperone-mediated protein complex assembly / acute-phase response / unfolded protein binding / protein folding / : / carbohydrate binding / blood microparticle / Amyloid fiber formation / innate immune response / calcium ion binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus
Similarity search - Function
: / Pentaxin, conserved site / Pentraxin domain signature. / Pentaxin family / Pentraxin / C-reactive protein / pentaxin family / Pentraxin-related / Pentraxin (PTX) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...: / Pentaxin, conserved site / Pentraxin domain signature. / Pentaxin family / Pentraxin / C-reactive protein / pentaxin family / Pentraxin-related / Pentraxin (PTX) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Serum amyloid P-component
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHohenester, E. / Pepys, M.B. / Wood, S.P.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Crystal structure of a decameric complex of human serum amyloid P component with bound dAMP.
Authors: Hohenester, E. / Hutchinson, W.L. / Pepys, M.B. / Wood, S.P.
#1: Journal: Nature / Year: 1994
Title: Structure of Pentameric Human Serum Amyloid P Component
Authors: Emsley, J. / White, H.E. / O'Hara, B.P. / Oliva, G. / Srinivasan, N. / Tickle, I.J. / Blundell, T.L. / Pepys, M.B. / Wood, S.P.
History
DepositionDec 4, 1996Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0May 29, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERUM AMYLOID P COMPONENT
B: SERUM AMYLOID P COMPONENT
C: SERUM AMYLOID P COMPONENT
D: SERUM AMYLOID P COMPONENT
E: SERUM AMYLOID P COMPONENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,46920
Polymers116,4125
Non-polymers2,05715
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-35 kcal/mol
Surface area38290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.030, 190.030, 119.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.3505, -0.8574, 0.3769), (0.9339, 0.3501, -0.072), (-0.0702, 0.3772, 0.9235)123.06, -92.17, -7.93
2given(-0.7068, -0.4514, 0.5447), (0.6552, -0.708, 0.2635), (0.2667, 0.5432, 0.7962)242.22, -8.37, -59.14
3given(-0.7096, 0.6532, 0.264), (-0.4508, -0.7089, 0.5425), (0.5415, 0.2659, 0.7975)193.16, 135.42999, -82.3
4given(0.3496, 0.9344, -0.0691), (-0.8562, 0.3485, 0.3814), (0.3805, -0.0742, 0.9218)42.51, 140.5, -46.07
DetailsSAP IS A PENTAMER OF IDENTICAL SUBUNITS.

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Components

#1: Protein
SERUM AMYLOID P COMPONENT


Mass: 23282.455 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: SERUM / References: UniProt: P02743
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE


Mass: 331.222 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H14N5O6P
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 4.24 Å3/Da / Density % sol: 71 %
Description: THE DIFFRACTION LIMIT IS VERY ANISOTROPIC (BETTER THAN 2.8 A ALONG A* AND B*, APPROXIMATELY 3.5 A ALONG C*)
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3 + 3 UL HANGING DROPS AT 277K PROTEIN SOLUTION: 20 MG/ML PROTEIN, 10 MM TRIS-HCL, PH 8.0, 140 MM NACL, 20 MM DAMP, 0.02 % NA-AZIDE. RESERVOIR SOLUTION: 100 MM BIS-TRIS PROPANE- HCL PH 8.0, ...Details: 3 + 3 UL HANGING DROPS AT 277K PROTEIN SOLUTION: 20 MG/ML PROTEIN, 10 MM TRIS-HCL, PH 8.0, 140 MM NACL, 20 MM DAMP, 0.02 % NA-AZIDE. RESERVOIR SOLUTION: 100 MM BIS-TRIS PROPANE- HCL PH 8.0, 20 MM CALCIUM CHLORIDE, 12-14 % (W/V) POLYETHYLENEGLYCOL 4000., vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
210 mMTris-HCl1drop
3140 mM1dropNaCl
420 mMdAMP1drop
50.02 %(w/v)1dropNaN3
60.1 Mbis-Tris propane-HCl1reservoir
714 %(w/v)PEG40001reservoir
820 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 366263 / % possible obs: 98 % / Redundancy: 6.9 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 6.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 1.4 / % possible all: 97.5
Reflection
*PLUS
Num. obs: 53133 / Num. measured all: 366263 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 97.5 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SAC WITHOUT WATER MOLECULES AND ACETATE IONS, ALL B-FACTORS SET TO 40 A**2

1sac


Resolution: 2.8→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: SEE REMARKS / Cross valid method: FREE R / σ(F): 0
Details: 15 THIN RESOLUTION SHELLS WERE DEFINED FOR THE CALCULATION OF THE FREE R VALUE USING XDLDATAMAN (CCP4).
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2478 4.8 %THIN RESOLUTION SHELLS
Rwork0.232 ---
obs0.232 48167 97.7 %-
Displacement parametersBiso mean: 50 Å2
Baniso -1Baniso -2Baniso -3
1-16.2 Å20 Å20 Å2
2--16.2 Å20 Å2
3----32.5 Å2
Refine analyzeLuzzati sigma a obs: 0.51 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8245 0 120 0 8365
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1
X-RAY DIFFRACTIONx_mcangle_it1.5
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)
11SEE REMARKSX-RAY DIFFRACTION0.071
22X-RAY DIFFRACTION0.076
33X-RAY DIFFRACTION0.07
44X-RAY DIFFRACTION0.064
LS refinement shellResolution: 2.8→2.92 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.432 354 5.5 %
Rwork0.454 5891 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.454

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