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- PDB-4avs: Structure of N-Acetyl-L-Proline bound to Serum Amyloid P Component -

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Basic information

Entry
Database: PDB / ID: 4avs
TitleStructure of N-Acetyl-L-Proline bound to Serum Amyloid P Component
ComponentsSERUM AMYLOID P-COMPONENT
KeywordsSUGAR BINDING PROTEIN / GLYCOPROTEIN / DISULFIDE BOND / LECTIN / METAL-BINDING
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
1-ACETYL-L-PROLINE / Serum amyloid P-component
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.399 Å
AuthorsKolstoe, S. / Wood, S.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Interaction of Serum Amyloid P Component with Hexanoyl Bis(D-Proline) (Cphpc)
Authors: Kolstoe, S.E. / Jenvey, M.C. / Purvis, A. / Light, M.E. / Thompson, D. / Hughes, P. / Pepys, M.B. / Wood, S.P.
History
DepositionMay 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Aug 31, 2016Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)118,70525
Polymers116,4125
Non-polymers2,29320
Water22,9691275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-145.3 kcal/mol
Surface area38210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.966, 69.937, 102.347
Angle α, β, γ (deg.)90.00, 96.97, 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) / Organ: SERUM / References: UniProt: P02743
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-N7P / 1-ACETYL-L-PROLINE / N-ACETYLPROLINE


Type: L-peptide linking / Mass: 157.167 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H11NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1275 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 8
Details: 0.06 M TRIS-HCL, PH 8, 16% PEG 550 MME, 0.01 M CACL2, 0.08 M NACL AND 0.1% NAN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→30.43 Å / Num. obs: 251592 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 8.47 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.2
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.5 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SAC

1sac


Resolution: 1.399→30.479 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 13.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1703 2003 0.8 %
Rwork0.1441 --
obs0.1443 251494 96.09 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.227 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 13.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.0774 Å20 Å2-0.084 Å2
2--0.2681 Å20 Å2
3---1.8093 Å2
Refinement stepCycle: LAST / Resolution: 1.399→30.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8245 0 135 1275 9655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018808
X-RAY DIFFRACTIONf_angle_d1.36512028
X-RAY DIFFRACTIONf_dihedral_angle_d13.7483228
X-RAY DIFFRACTIONf_chiral_restr0.0881299
X-RAY DIFFRACTIONf_plane_restr0.0071546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3993-1.43430.20561500.166617367X-RAY DIFFRACTION94
1.4343-1.47310.21831360.174517686X-RAY DIFFRACTION96
1.4731-1.51640.19761430.153817684X-RAY DIFFRACTION96
1.5164-1.56530.14121420.130817768X-RAY DIFFRACTION96
1.5653-1.62130.18031400.10817871X-RAY DIFFRACTION97
1.6213-1.68620.14491570.106417886X-RAY DIFFRACTION97
1.6862-1.76290.14491360.10717959X-RAY DIFFRACTION97
1.7629-1.85590.13531460.108118040X-RAY DIFFRACTION97
1.8559-1.97210.1971310.153618086X-RAY DIFFRACTION98
1.9721-2.12430.14231600.12418145X-RAY DIFFRACTION98
2.1243-2.33810.19591410.152118308X-RAY DIFFRACTION98
2.3381-2.67620.17111460.141218341X-RAY DIFFRACTION99
2.6762-3.3710.15891440.147618382X-RAY DIFFRACTION98
3.371-30.4860.17991310.17815968X-RAY DIFFRACTION84

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