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- PDB-3pvo: Monoclinic form of Human C-Reactive Protein -

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Basic information

Entry
Database: PDB / ID: 3pvo
TitleMonoclinic form of Human C-Reactive Protein
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: 3 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 9, 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)462,96460
Polymers461,36120
Non-polymers1,60340
Water7,152397
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)115,74115
Polymers115,3405
Non-polymers40110
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-138 kcal/mol
Surface area41440 Å2
MethodPISA
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)115,74115
Polymers115,3405
Non-polymers40110
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-149 kcal/mol
Surface area41590 Å2
MethodPISA
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)115,74115
Polymers115,3405
Non-polymers40110
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-147 kcal/mol
Surface area41230 Å2
MethodPISA
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)115,74115
Polymers115,3405
Non-polymers40110
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-150 kcal/mol
Surface area41410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.600, 143.200, 161.200
Angle α, β, γ (deg.)90.00, 89.70, 90.00
Int Tables number4
Space group name H-MP1211

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.44 Å3/Da / Density % sol: 49.62 %
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: BM30A / Wavelength: 0.979689 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2009
RadiationMonochromator: two crystals monochromator between two cylindrical parabolic mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979689 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 86781 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.96 % / Rsym value: 0.153 / Net I/σ(I): 6.7
Reflection shellResolution: 3→3.08 Å / Redundancy: 1.79 % / Mean I/σ(I) obs: 1.99 / % possible all: 92.6

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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: 3→20 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.774 / SU B: 24.462 / SU ML: 0.453 / Cross valid method: THROUGHOUT / ESU R Free: 0.557 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28521 4380 5.1 %RANDOM
Rwork0.22651 ---
obs0.22946 82034 97.81 %-
all-82032 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.827 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20.53 Å2
2--0.76 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32640 0 40 397 33077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02233578
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.94645655
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06954099
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70324.2471460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.365155440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.77115120
X-RAY DIFFRACTIONr_chiral_restr0.1040.24939
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02125596
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4741.520478
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89233255
X-RAY DIFFRACTIONr_scbond_it1.04313100
X-RAY DIFFRACTIONr_scangle_it1.8774.512400
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.001→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 319 -
Rwork0.264 5746 -
obs--94.93 %

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