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- PDB-2a3y: Pentameric crystal structure of human serum amyloid P-component b... -

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Basic information

Entry
Database: PDB / ID: 2a3y
TitlePentameric crystal structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2carboxy-2-methyl-1,3-dioxane]-5-yloxycarbamoyl}-ethane.
ComponentsSerum amyloid P-component
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


negative regulation by host of viral exo-alpha-sialidase activity / negative regulation by host of viral glycoprotein metabolic process / negative regulation of exo-alpha-sialidase activity / 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 / negative regulation of viral entry into host cell / virion binding ...negative regulation by host of viral exo-alpha-sialidase activity / negative regulation by host of viral glycoprotein metabolic process / negative regulation of exo-alpha-sialidase activity / 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 / negative regulation of viral entry into host cell / virion binding / negative regulation of acute inflammatory response / chaperone-mediated protein complex assembly / acute-phase response / unfolded protein binding / protein folding / carbohydrate binding / collagen-containing extracellular matrix / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-CPJ / Serum amyloid P-component
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHo, J.G. / Kitov, P.I. / Paszkiewicz, E. / Sadowska, J. / Bundle, D.R. / Ng, K.K.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Ligand-assisted Aggregation of Proteins: DIMERIZATION OF SERUM AMYLOID P COMPONENT BY BIVALENT LIGANDS.
Authors: Ho, J.G. / Kitov, P.I. / Paszkiewicz, E. / Sadowska, J. / Bundle, D.R. / Ng, K.K.
History
DepositionJun 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)118,99520
Polymers116,4125
Non-polymers2,58315
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9950 Å2
ΔGint-139 kcal/mol
Surface area38210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.715, 69.956, 101.367
Angle α, β, γ (deg.)90.00, 97.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Serum amyloid P-component / SAP / 9.5S alpha-1-glycoprotein


Mass: 23282.455 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / 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-CPJ / BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBAMOYL}-ETHANE


Mass: 436.368 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H24N2O12
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: sodium actetate, calcium acetate, PEG 8000, PEG 400, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115872 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 18, 2003 / Details: Double crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115872 Å / Relative weight: 1
ReflectionResolution: 2→50.7 Å / Num. all: 84221 / Num. obs: 84221 / % possible obs: 94.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 17.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 6.3 / Num. unique all: 8126 / Rsym value: 0.172 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LGN

1lgn


Resolution: 2→50.6 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.902 / SU B: 4.117 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24965 4216 5 %RANDOM
Rwork0.21567 ---
all0.21738 84201 --
obs0.21738 79985 94.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.732 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å20.2 Å2
2---1.11 Å20 Å2
3---2.38 Å2
Refinement stepCycle: LAST / Resolution: 2→50.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8245 0 75 478 8798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0218550
X-RAY DIFFRACTIONr_angle_refined_deg1.0861.95711635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95551015
X-RAY DIFFRACTIONr_chiral_restr0.0710.21250
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026565
X-RAY DIFFRACTIONr_nbd_refined0.1730.23686
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0780.2510
X-RAY DIFFRACTIONr_metal_ion_refined0.0180.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.218
X-RAY DIFFRACTIONr_mcbond_it0.7351.55085
X-RAY DIFFRACTIONr_mcangle_it1.32128260
X-RAY DIFFRACTIONr_scbond_it2.22633465
X-RAY DIFFRACTIONr_scangle_it3.1694.53375
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0.297 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 316 -
Rwork0.22 5698 -
obs-17285 91.8 %
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)
10.54190.03570.09640.3644-0.00160.82570.07390.067-0.1067-0.0115-0.00850.09830.0626-0.0304-0.06540.06270.0319-0.02370.0788-0.03390.2032-10.24824.134728.2142
21.1694-0.0665-0.13440.38570.06170.40560.05190.1996-0.136-0.0761-0.03850.1379-0.0113-0.1053-0.01340.1610.066-0.0580.1891-0.09230.16669.02411.3804-2.938
30.6265-0.0930.30450.6472-0.04080.88370.00820.0982-0.067-0.1242-0.06760.0275-0.027-0.00630.05940.12460.02850.01810.0849-0.03660.023844.4618-3.59595.822
40.4925-0.0063-0.20610.59090.02350.89610.0226-0.0072-0.004-0.0134-0.0245-0.04150.02340.03440.00190.0547-0.00440.00640.0527-0.00210.038447.2559-3.65742.5835
51.3938-0.1059-0.01220.4241-0.0450.45220.0969-0.12830.04270.06-0.01370.116-0.01660.009-0.08320.076-0.02690.0480.0589-0.03260.10913.35321.493256.3981
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2041 - 204
2X-RAY DIFFRACTION2BB1 - 2041 - 204
3X-RAY DIFFRACTION3CC1 - 2041 - 204
4X-RAY DIFFRACTION4DD1 - 2041 - 204
5X-RAY DIFFRACTION5EE1 - 2041 - 204

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