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- PDB-2a3w: Decameric structure of human serum amyloid P-component bound to B... -

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Basic information

Entry
Database: PDB / ID: 2a3w
TitleDecameric structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2-carboxy-2-methyl-1,3-dioxane]-5-yloxycarbamoyl}-ethane
ComponentsSerum amyloid P-component
KeywordsMETAL BINDING PROTEIN / Multivalent ligand complex
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: 2.2 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 / Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: refine_ls_shell
Item: _refine_ls_shell.number_reflns_obs / _refine_ls_shell.percent_reflns_obs
Revision 1.4Jan 22, 2020Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.5Aug 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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

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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
F: Serum amyloid P-component
G: Serum amyloid P-component
H: Serum amyloid P-component
I: Serum amyloid P-component
J: Serum amyloid P-component
K: Serum amyloid P-component
L: Serum amyloid P-component
M: Serum amyloid P-component
N: Serum amyloid P-component
O: Serum amyloid P-component
P: Serum amyloid P-component
Q: Serum amyloid P-component
R: Serum amyloid P-component
S: Serum amyloid P-component
T: Serum amyloid P-component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)471,61670
Polymers465,64920
Non-polymers5,96750
Water42,8402378
1
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
F: Serum amyloid P-component
G: Serum amyloid P-component
H: Serum amyloid P-component
I: Serum amyloid P-component
J: Serum amyloid P-component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,80835
Polymers232,82510
Non-polymers2,98325
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: Serum amyloid P-component
L: Serum amyloid P-component
M: Serum amyloid P-component
N: Serum amyloid P-component
O: Serum amyloid P-component
P: Serum amyloid P-component
Q: Serum amyloid P-component
R: Serum amyloid P-component
S: Serum amyloid P-component
T: Serum amyloid P-component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,80835
Polymers232,82510
Non-polymers2,98325
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.712, 105.325, 146.007
Angle α, β, γ (deg.)86.53, 78.15, 76.78
Int Tables number1
Space group name H-MP1
DetailsThere are two decameric complexes of hSAP in the asymmetric unit

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Components

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


Mass: 23282.455 Da / Num. of mol.: 20 / 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.: 40 / 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.: 10 / Source method: obtained synthetically / Formula: C16H24N2O12
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2378 / 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: 3 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, PEG 400, sodium acetate, calcium acetate, sorbitol, 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: 1.115879 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2004
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115879 Å / Relative weight: 1
ReflectionResolution: 2.2→60 Å / Num. all: 269382 / Num. obs: 269382 / % possible obs: 97.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 15.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 26464 / Rsym value: 0.231 / % possible all: 95.6

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Processing

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

1lgn


Resolution: 2.2→100 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.192 / SU ML: 0.132 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 13598 5.1 %RANDOM
Rwork0.18798 ---
all0.19005 269370 --
obs0.19005 269370 97.11 %-
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: 17.077 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å2-0.78 Å20.35 Å2
2--0.79 Å21.14 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32980 0 340 2378 35698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02134250
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.95946620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24254060
X-RAY DIFFRACTIONr_chiral_restr0.0750.25000
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0226380
X-RAY DIFFRACTIONr_nbd_refined0.1790.215312
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.22172
X-RAY DIFFRACTIONr_metal_ion_refined0.0070.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.28
X-RAY DIFFRACTIONr_mcbond_it0.8271.520340
X-RAY DIFFRACTIONr_mcangle_it1.494233040
X-RAY DIFFRACTIONr_scbond_it2.629313910
X-RAY DIFFRACTIONr_scangle_it3.9014.513580
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.293 1046
Rwork0.23 18464
obs-26464
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)
12.22780.13950.0350.9574-0.17570.8214-0.02590.05740.1546-0.0380.03690.0312-0.1327-0.0682-0.0110.09630.0169-0.0280.0177-0.03790.0824-4.10127.494-14.661
21.11930.4852-0.02651.775-0.6811.1269-0.0342-0.03790.0673-0.00310.09820.2508-0.0581-0.2528-0.0640.02370.0007-0.03630.1909-0.03580.1259-30.6062.978-6.8
31.5523-0.23060.1581.1314-0.50011.1419-0.06-0.0105-0.2070.076-0.00260.09860.1365-0.13720.06260.1316-0.0390.02490.1166-0.04120.1346-15.016-25.75510.406
41.61970.538-0.06511.7013-0.37190.8605-0.0222-0.1704-0.14310.1265-0.1296-0.24690.12810.13560.15180.12940.0629-0.03830.13150.06730.182721.195-18.76413.39
51.0487-0.49020.11981.499-0.59220.87670.0072-0.10260.06570.1331-0.1227-0.3252-0.06980.22070.11550.0596-0.0204-0.05490.13460.0020.215628.00314.023-2.312
61.1576-0.04410.06121.8788-0.53611.17220.04290.0390.0126-0.0807-0.0543-0.2380.04180.25870.01140.0518-0.0278-0.02880.1507-0.07380.174137.929-14.532-31.591
72.07190.6854-0.13351.3731-0.01570.805-0.0392-0.1925-0.28810.05590.0255-0.19120.20020.14230.01370.18960.0282-0.04390.0933-0.01090.15518.016-43.564-20.206
81.1886-0.19450.27741.2847-0.53331.0322-0.0141-0.0004-0.09940.02280.04140.17960.1572-0.1848-0.02730.1504-0.05490.02280.0696-0.03670.1347-17.158-37.699-30.212
91.2880.6555-0.30881.8977-0.47950.9228-0.03270.20410.1363-0.16440.06640.2547-0.0037-0.1748-0.03370.10090.0198-0.04940.13210.00090.1822-19.111-5.079-47.387
102.2048-0.07220.06281.0728-0.13620.82640.01290.12640.2223-0.11920.0217-0.0354-0.13610.0028-0.03460.1582-0.03410.00930.045-0.01240.151214.9719.229-48.369
112.24830.6366-1.11611.3157-0.7381.88620.24240.30340.4484-0.08790.04510.1686-0.274-0.2912-0.28750.43780.08510.09390.21490.0930.2303-40.11773.15155.809
120.8855-0.3087-0.06771.7304-0.31441.397-0.02860.0022-0.0406-0.02660.0340.110.0514-0.187-0.00540.2971-0.06480.05860.0895-0.03220.1311-43.11148.61783.29
132.9314-0.141-0.68860.8878-0.23441.1706-0.0969-0.3461-0.25950.1868-0.0454-0.06470.17550.34120.14220.4370.04430.02810.1770.02980.1794-9.25335.77390.98
141.2928-0.0234-0.31742.0413-0.82042.3048-0.0505-0.0815-0.04170.2702-0.1195-0.3467-0.09710.57470.170.2988-0.0505-0.06350.40650.00540.247814.81352.24368.219
152.0276-0.0943-0.40181.2053-0.4811.9060.16510.05640.19610.1774-0.0311-0.073-0.36130.155-0.1340.3656-0.08970.09030.15970.0050.1513-4.45575.10646.379
161.71270.1216-0.7051.2093-0.23461.4861-0.01540.18910.0899-0.1440.14780.2958-0.1624-0.1743-0.13240.19460.0385-0.05810.18670.0460.1826-36.05346.93122.664
171.4439-0.24480.42921.6384-0.61.3602-0.08350.0430.0572-0.12850.0254-0.1926-0.20410.32420.05810.1415-0.04710.03080.3638-0.10380.07390.32440.55923.018
181.7790.7677-0.74321.362-0.75041.6886-0.0501-0.001-0.2791-0.0313-0.0419-0.24220.17310.44560.0920.0980.1219-0.01110.4216-0.06620.17657.08115.56449.496
192.34060.1105-0.28850.8181-0.16551.51060.0346-0.0703-0.23690.0831-0.01190.01270.30580.1212-0.02260.24790.03210.01430.0941-0.00660.1377-24.9546.94365.838
201.3294-0.04750.10081.8441-1.24352.59740.0852-0.00040.07870.12310.150.41130.0297-0.3952-0.23520.11410.01690.05260.20640.04660.313-51.62926.39349.198
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
6X-RAY DIFFRACTION6FF1 - 2041 - 204
7X-RAY DIFFRACTION7GG1 - 2041 - 204
8X-RAY DIFFRACTION8HH1 - 2041 - 204
9X-RAY DIFFRACTION9II1 - 2041 - 204
10X-RAY DIFFRACTION10JJ1 - 2041 - 204
11X-RAY DIFFRACTION11KK1 - 2041 - 204
12X-RAY DIFFRACTION12LL1 - 2041 - 204
13X-RAY DIFFRACTION13MM1 - 2041 - 204
14X-RAY DIFFRACTION14NN1 - 2041 - 204
15X-RAY DIFFRACTION15OO1 - 2041 - 204
16X-RAY DIFFRACTION16PP1 - 2041 - 204
17X-RAY DIFFRACTION17QQ1 - 2041 - 204
18X-RAY DIFFRACTION18RR1 - 2041 - 204
19X-RAY DIFFRACTION19SS1 - 2041 - 204
20X-RAY DIFFRACTION20TT1 - 2041 - 204

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