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- PDB-3pvn: Triclinic form of Human C-Reactive Protein in complex with Zinc -

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Basic information

Entry
Database: PDB / ID: 3pvn
TitleTriclinic form of Human C-Reactive Protein in complex with Zinc
ComponentsC-reactive protein
KeywordsIMMUNE SYSTEM / pentraxin family
Function / homology
Function and homology information


regulation of interleukin-8 production / opsonization / complement component C1q complex binding / low-density lipoprotein particle binding / vasoconstriction / choline binding / negative regulation of mononuclear cell proliferation / Classical antibody-mediated complement activation / low-density lipoprotein particle receptor binding / negative regulation of macrophage derived foam cell differentiation ...regulation of interleukin-8 production / opsonization / complement component C1q complex binding / low-density lipoprotein particle binding / vasoconstriction / choline binding / negative regulation of mononuclear cell proliferation / Classical antibody-mediated complement activation / low-density lipoprotein particle receptor binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / positive regulation of superoxide anion generation / acute-phase response / defense response to Gram-positive bacterium / inflammatory response / innate immune response / calcium ion binding / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsGuillon, C. / Mavoungou Bigouagou, U. / Jeannin, P. / Delneste, Y. / Gouet, P.
CitationJournal: Protein Pept.Lett. / Year: 2014
Title: A Staggered Decameric Assembly of Human C-Reactive Protein Stabilized by Zinc Ions Revealed by X-ray Crystallography.
Authors: Guillon, C. / Bigouagou, U.M. / Folio, C. / Jeannin, P. / Delneste, Y. / Gouet, P.
History
DepositionDec 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-reactive protein
B: C-reactive protein
C: C-reactive protein
D: C-reactive protein
E: C-reactive protein
F: C-reactive protein
G: C-reactive protein
H: C-reactive protein
I: C-reactive protein
J: C-reactive protein
K: C-reactive protein
L: C-reactive protein
M: C-reactive protein
N: C-reactive protein
O: C-reactive protein
P: C-reactive protein
Q: C-reactive protein
R: C-reactive protein
S: C-reactive protein
T: C-reactive protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)463,29165
Polymers461,36120
Non-polymers1,93045
Water54,2433011
1
A: C-reactive protein
B: C-reactive protein
C: C-reactive protein
D: C-reactive protein
E: C-reactive protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,80616
Polymers115,3405
Non-polymers46611
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: C-reactive protein
G: C-reactive protein
H: C-reactive protein
I: C-reactive protein
J: C-reactive protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,80616
Polymers115,3405
Non-polymers46611
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: C-reactive protein
L: C-reactive protein
M: C-reactive protein
N: C-reactive protein
O: C-reactive protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,80616
Polymers115,3405
Non-polymers46611
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: C-reactive protein
Q: C-reactive protein
R: C-reactive protein
S: C-reactive protein
T: C-reactive protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,87217
Polymers115,3405
Non-polymers53212
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.300, 96.400, 160.400
Angle α, β, γ (deg.)79.90, 77.10, 69.40
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
C-reactive protein / C-reactive protein(1-205)


Mass: 23068.039 Da / Num. of mol.: 20 / Fragment: UNP residues 19-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRP, PTX1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02741
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3011 / 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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8
Details: 12% PEG 4000, 0.1M Tris-Hcl, 0.2M MgCl2, 0.05M LiCl, pH 8.0, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2008
RadiationMonochromator: horizontally diffracting Si (111) monochromator and Pt coated mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.98→20 Å / Num. all: 275048 / Num. obs: 275047 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.94 % / Biso Wilson estimate: 29.7 Å2 / Rsym value: 0.062 / Net I/σ(I): 9.7
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 1.85 % / Mean I/σ(I) obs: 2.96 / Num. unique all: 19869 / Rsym value: 0.321 / % possible all: 91.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LJ7

1lj7


Resolution: 1.98→19.92 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.076 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23551 13541 4.9 %RANDOM
Rwork0.17564 ---
all0.19156 261507 --
obs0.17857 261507 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.649 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å2-0.34 Å20.24 Å2
2---0.16 Å20.27 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.98→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32640 0 45 3011 35696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02233580
X-RAY DIFFRACTIONr_angle_refined_deg1.9381.94645660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84354100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54124.2471460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.213155440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.99815120
X-RAY DIFFRACTIONr_chiral_restr0.1680.24940
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02125600
X-RAY DIFFRACTIONr_mcbond_it1.2761.520480
X-RAY DIFFRACTIONr_mcangle_it2.248233260
X-RAY DIFFRACTIONr_scbond_it3.448313100
X-RAY DIFFRACTIONr_scangle_it5.2494.512400
LS refinement shellResolution: 1.982→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 575 -
Rwork0.225 13439 -
obs-13439 100 %

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