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- PDB-4pbp: crystal structure of zebrafish short-chain pentraxin protein -

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Basic information

Entry
Database: PDB / ID: 4pbp
Titlecrystal structure of zebrafish short-chain pentraxin protein
ComponentsC-reactive protein
KeywordsIMMUNE SYSTEM / acute phase protein / pentraxin
Function / homology
Function and homology information


cholesterol binding / acute-phase response / defense response to virus / extracellular region / metal ion binding
Similarity search - Function
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
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.648 Å
AuthorsChen, R. / Qi, J.X. / George, F.G. / Xia, C.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Crystal structures for short-chain pentraxin from zebrafish demonstrate a cyclic trimer with new recognition and effector faces.
Authors: Chen, R. / Qi, J. / Yuan, H. / Wu, Y. / Hu, W. / Xia, C.
History
DepositionApr 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_symm_contact / refine_hist / struct_conn / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _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_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-reactive protein
B: C-reactive protein
C: C-reactive protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,42112
Polymers71,9043
Non-polymers5179
Water14,628812
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-81 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.623, 153.623, 62.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein C-reactive protein


Mass: 23967.977 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: crp / Production host: Escherichia coli (E. coli) / References: UniProt: G9D324
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 812 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.085M HEPES sodium, 8.5% v/v 2-Propanol, 17% w/v Polyethylene glycol 4000, 15% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.648→50 Å / Num. obs: 100591 / % possible obs: 99.4 % / Redundancy: 8 % / Net I/σ(I): 18.836

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PBO

4pbo


Resolution: 1.648→39.137 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.171 5025 5 %
Rwork0.153 --
obs0.1539 100588 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.648→39.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5009 0 24 812 5845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015187
X-RAY DIFFRACTIONf_angle_d1.3957061
X-RAY DIFFRACTIONf_dihedral_angle_d12.7611863
X-RAY DIFFRACTIONf_chiral_restr0.107775
X-RAY DIFFRACTIONf_plane_restr0.006908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.648-1.66640.21761800.17952962X-RAY DIFFRACTION94
1.6664-1.6860.20981890.16773198X-RAY DIFFRACTION100
1.686-1.70650.22811640.16443169X-RAY DIFFRACTION100
1.7065-1.72810.19911680.16593204X-RAY DIFFRACTION100
1.7281-1.75090.18051590.16033166X-RAY DIFFRACTION100
1.7509-1.77480.1991550.16123188X-RAY DIFFRACTION100
1.7748-1.80020.19321630.16133170X-RAY DIFFRACTION100
1.8002-1.82710.18631770.15823179X-RAY DIFFRACTION100
1.8271-1.85560.18691790.15583169X-RAY DIFFRACTION100
1.8556-1.8860.19071400.15353249X-RAY DIFFRACTION100
1.886-1.91860.16811610.15183171X-RAY DIFFRACTION100
1.9186-1.95340.17721710.14913201X-RAY DIFFRACTION100
1.9534-1.9910.19171510.14523168X-RAY DIFFRACTION100
1.991-2.03170.17941450.15053232X-RAY DIFFRACTION100
2.0317-2.07580.1821680.15093226X-RAY DIFFRACTION100
2.0758-2.12410.17621770.14573164X-RAY DIFFRACTION100
2.1241-2.17720.15381750.14493171X-RAY DIFFRACTION99
2.1772-2.23610.18691640.14663211X-RAY DIFFRACTION99
2.2361-2.30190.17531800.15763197X-RAY DIFFRACTION100
2.3019-2.37620.18051690.15783176X-RAY DIFFRACTION100
2.3762-2.46110.17241830.15863165X-RAY DIFFRACTION100
2.4611-2.55960.17451430.16173220X-RAY DIFFRACTION100
2.5596-2.67610.21561570.16253224X-RAY DIFFRACTION99
2.6761-2.81710.181520.15993210X-RAY DIFFRACTION99
2.8171-2.99360.17361750.15523183X-RAY DIFFRACTION99
2.9936-3.22460.151700.15753194X-RAY DIFFRACTION100
3.2246-3.54890.15751670.14933208X-RAY DIFFRACTION99
3.5489-4.0620.15361900.13363185X-RAY DIFFRACTION99
4.062-5.11590.12691740.13173196X-RAY DIFFRACTION98
5.1159-39.14770.1731790.17823207X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 9.9299 Å / Origin y: -61.4688 Å / Origin z: 11.1661 Å
111213212223313233
T0.2035 Å2-0.0094 Å2-0.0002 Å2-0.2054 Å2-0.0017 Å2--0.2029 Å2
L0.291 °20.0602 °20.0608 °2-0.1642 °20.0291 °2--0.171 °2
S-0.0035 Å °-0.0033 Å °0.0076 Å °0.0129 Å °-0.0124 Å °0.0076 Å °-0.0342 Å °-0.0015 Å °-0 Å °
Refinement TLS groupSelection details: all

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