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- PDB-1sac: THE STRUCTURE OF PENTAMERIC HUMAN SERUM AMYLOID P COMPONENT -

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Basic information

Entry
Database: PDB / ID: 1sac
TitleTHE STRUCTURE OF PENTAMERIC HUMAN SERUM AMYLOID P COMPONENT
ComponentsSERUM AMYLOID P COMPONENT
KeywordsAMYLOID PROTEIN
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
ACETIC ACID / Serum amyloid P-component
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsWhite, H.E. / Emsley, J. / O'Hara, B.P. / Oliva, G. / Srinivasan, N. / Tickle, I.J. / Blundell, T.L. / Pepys, M.B. / Wood, S.P.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: A Pentameric Form of Human Serum Amyloid P Component: Crystallization, X-Ray Diffraction and Neutron Scattering Studies
Authors: Wood, S.P. / Oliva, G. / O'Hara, B.P. / White, H.E. / Blundell, T.L. / Perkins, S.J. / Sardharwalla, I. / Pepys, M.P.
#2: Journal: J.Cryst.Growth / Year: 1988
Title: Crystallization of Human Serum Amyloid P Component (Sap)
Authors: O'Hara, B.P. / Wood, S.P. / Oliva, G. / White, H.E. / Pepys, M.B.
#3: Journal: J.Biochem.(Tokyo) / Year: 1986
Title: Isolation and Characterization of the Complete Complementary and Genomic DNA Sequences of Human Serum
Authors: Ohnishi, S. / Maeda, S. / Shimada, K. / Arao, T.
History
DepositionJan 27, 1994Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET STRANDS A1_ AND A2_ IN ALL FIVE CHAINS ARE DISCONNECTED BUT FORM A CONTINUOUS STRAND IN THE STRUCTURE.

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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)117,05319
Polymers116,4125
Non-polymers64114
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-111 kcal/mol
Surface area38190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.900, 99.300, 96.700
Angle α, β, γ (deg.)90.00, 95.90, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 89
2: PHE B 33 - THR B 34 OMEGA = 145.17 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: CIS PROLINE - PRO B 89 / 4: CIS PROLINE - PRO C 89 / 5: CIS PROLINE - PRO D 89 / 6: CIS PROLINE - PRO E 89
7: PRO E 129 - LYS E 130 OMEGA = 148.51 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.499031, -0.291022, 0.816257), (-0.320116, 0.813396, 0.485709), (-0.805291, -0.50368, 0.312749)6.60979, 4.55958, 41.24557
2given(-0.310617, -0.777136, 0.547336), (-0.819014, 0.51106, 0.260832), (-0.482423, -0.367257, -0.795229)41.93763, 26.04455, 47.15978
3given(-0.354165, -0.796676, -0.48977), (-0.766242, 0.547449, -0.336411), (0.536135, 0.256137, -0.804334)57.58439, 34.00153, 9.05447
4given(0.495935, -0.324849, -0.805309), (-0.289427, 0.812525, -0.505999), (0.818707, 0.48402, 0.308939)31.4469, 19.3346, -20.40029
DetailsSAP IS A PENTAMER OF IDENTICAL POLYPEPTIDE CHAINS. THE COORDINATES OF ALL FIVE CHAINS ARE INCLUDED IN THIS ENTRY AND HAVE BEEN ASSIGNED CHAIN INDICATORS *A*, *B*, *C*, *D*, AND *E*. THE TRANSFORMATIONS GIVEN IN THE *MTRIX* RECORDS BELOW REPRESENT THE NON-CRYSTALLOGRAPHIC FIVE-FOLD AXIS. THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN A WHEN APPLIED TO CHAIN B. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN A WHEN APPLIED TO CHAIN C. THE TRANSFORMATION PRESENTED ON *MTRIX 3* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN A WHEN APPLIED TO CHAIN D. THE TRANSFORMATION PRESENTED ON *MTRIX 4* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN A WHEN APPLIED TO CHAIN E.

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Components

#1: Protein
SERUM AMYLOID P COMPONENT


Mass: 23282.455 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
Has protein modificationY
Sequence detailsSEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: SAMP_HUMAN NAME NUMBER NAME CHAIN SEQ PRO 101 SER A 82 PRO 101 SER B 82 PRO 101 SER C 82 PRO 101 SER D 82 PRO 101 SER E 82 THE SEQUENCE BUILT INTO THIS STRUCTURE IS THE AMENDED VERSION WHERE RESIDUE 82 IS A SERINE. SEE REFERENCE 3.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.46 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: unknown
Details: taken from Wood, S.P. et al (1988). J. Mol. Biol., 202, 169-173.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
127.7 mg/mlprotein11in 10 mM Tris-HCl, 10 mM EDTA, 0.14 M NaCl
21 Msodium acetate12
3200 mMcalcium acetate12
450 %(w/v)PEG600012

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / % possible obs: 93.6 %

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Processing

Software
NameClassification
X-PLORmodel building
RESTRAINrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.179 -
obs0.179 78910
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8245 0 10 16 8271
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg3.45
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Num. reflection all: 78910 / Rfactor all: 0.179 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.45

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