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- PDB-4ayu: Structure of N-Acetyl-D-Proline bound to serum amyloid P component -

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Basic information

Entry
Database: PDB / ID: 4ayu
TitleStructure of N-Acetyl-D-Proline bound to serum amyloid P component
ComponentsSERUM AMYLOID P-COMPONENT
KeywordsSUGAR BINDING PROTEIN / LECTIN
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
N-ACETYL-D-PROLINE / Serum amyloid P-component
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHughes, P. / Kolstoe, S.E. / 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
DepositionJun 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3Jul 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 1.4Dec 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 1.5Oct 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)119,16530
Polymers116,4125
Non-polymers2,75325
Water24,5361362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10610 Å2
ΔGint-85.6 kcal/mol
Surface area38670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.420, 70.555, 99.055
Angle α, β, γ (deg.)90.00, 96.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 10 molecules ABCDE

#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
#4: 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

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Non-polymers , 4 types, 1382 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-N8P / N-ACETYL-D-PROLINE


Type: D-peptide linking / Mass: 157.167 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H11NO3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1362 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.62 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 8
Details: 60 MM TRIS-HCL PH 8.0, 10 MM CACL2, 84 MM NACL, 20% GLYCEROL V/V, 17% PEG550 MME V/V

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→31.24 Å / Num. obs: 198644 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.1
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2.6 / % possible all: 91

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Processing

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

1sac


Resolution: 1.5→28.663 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 15.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1676 1995 1 %
Rwork0.1547 --
obs0.1548 198604 96.25 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.907 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.1292 Å20 Å20.0008 Å2
2---0.1383 Å20 Å2
3---0.0092 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8245 0 165 1362 9772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078813
X-RAY DIFFRACTIONf_angle_d1.2612032
X-RAY DIFFRACTIONf_dihedral_angle_d13.4353226
X-RAY DIFFRACTIONf_chiral_restr0.0791307
X-RAY DIFFRACTIONf_plane_restr0.0051531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5002-1.53770.24011330.243213024X-RAY DIFFRACTION90
1.5377-1.57930.22991330.220713260X-RAY DIFFRACTION91
1.5793-1.62580.22291330.206313588X-RAY DIFFRACTION93
1.6258-1.67820.2261330.192213798X-RAY DIFFRACTION95
1.6782-1.73820.18691330.179213995X-RAY DIFFRACTION96
1.7382-1.80780.17031330.159614102X-RAY DIFFRACTION97
1.8078-1.890.19281330.150214175X-RAY DIFFRACTION97
1.89-1.98970.18671330.139314256X-RAY DIFFRACTION98
1.9897-2.11430.15571330.135814299X-RAY DIFFRACTION98
2.1143-2.27750.1562660.136714257X-RAY DIFFRACTION98
2.2775-2.50650.14751330.137914409X-RAY DIFFRACTION98
2.5065-2.8690.15261330.146214374X-RAY DIFFRACTION98
2.869-3.61350.1741330.141814215X-RAY DIFFRACTION97
3.6135-28.66840.14641330.160214857X-RAY DIFFRACTION99

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