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- PDB-4pbo: Crystal structure of zebrafish short-chain pentraxin protein with... -

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Basic information

Entry
Database: PDB / ID: 4pbo
TitleCrystal structure of zebrafish short-chain pentraxin protein without calcium ions
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 / SAD / Resolution: 1.701 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 1.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-reactive protein


Theoretical massNumber of molelcules
Total (without water)23,5601
Polymers23,5601
Non-polymers00
Water4,197233
1
A: C-reactive protein

A: C-reactive protein

A: C-reactive protein


Theoretical massNumber of molelcules
Total (without water)70,6813
Polymers70,6813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)114.745, 114.745, 61.023
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-376-

HOH

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Components

#1: Protein C-reactive protein


Mass: 23560.494 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 3.28 Å3/Da / Density % sol: 62.52 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.085M HEPES, 1.7% v/v polyethylene glycol 400, 1.7M ammonium sulphate, 15% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.98048 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98048 Å / Relative weight: 1
ReflectionResolution: 1.7→26 Å / Num. obs: 32265 / % possible obs: 98 % / Redundancy: 10.8 % / Net I/σ(I): 31.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 7.111 / Rsym value: 0.274 / % possible all: 92

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.5_2) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 1.701→26 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.186 1554 5.04 %
Rwork0.1735 --
obs0.1742 30815 93.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.902 Å2 / ksol: 0.428 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.0515 Å20 Å20 Å2
2---11.0515 Å2-0 Å2
3---22.1029 Å2
Refinement stepCycle: LAST / Resolution: 1.701→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 0 233 1897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061706
X-RAY DIFFRACTIONf_angle_d1.0332322
X-RAY DIFFRACTIONf_dihedral_angle_d14.693599
X-RAY DIFFRACTIONf_chiral_restr0.072256
X-RAY DIFFRACTIONf_plane_restr0.004298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.701-1.75540.18941150.18272276X-RAY DIFFRACTION80
1.7554-1.81820.19961210.17652474X-RAY DIFFRACTION86
1.8182-1.89090.20341390.17342535X-RAY DIFFRACTION90
1.8909-1.9770.17421460.16122637X-RAY DIFFRACTION93
1.977-2.08120.19891410.15642672X-RAY DIFFRACTION95
2.0812-2.21150.18441380.16282814X-RAY DIFFRACTION98
2.2115-2.38210.20421480.16672781X-RAY DIFFRACTION98
2.3821-2.62160.18821810.16922770X-RAY DIFFRACTION99
2.6216-3.00050.18631420.17072846X-RAY DIFFRACTION99
3.0005-3.77850.16861570.16022804X-RAY DIFFRACTION99
3.7785-26.00350.17771260.18012652X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: -2.8936 Å / Origin y: -20.1554 Å / Origin z: -22.2289 Å
111213212223313233
T0.2428 Å2-0.0006 Å2-0.0242 Å2-0.2228 Å2-0.0053 Å2--0.2246 Å2
L0.85 °20.5679 °2-0.1221 °2-0.8266 °2-0.1542 °2--0.3021 °2
S-0.0295 Å °0.034 Å °-0.2051 Å °0.0235 Å °0.0388 Å °-0.0671 Å °0.0004 Å °0.0119 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

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