[English] 日本語
Yorodumi
- PDB-3pvo: Monoclinic form of Human C-Reactive Protein -

+
Open data


ID or keywords:

Loading...

-
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 / negative regulation of mononuclear cell proliferation / vasoconstriction / choline binding / low-density lipoprotein particle receptor binding / Classical antibody-mediated complement activation / negative regulation of macrophage derived foam cell differentiation ...regulation of interleukin-8 production / opsonization / complement component C1q complex binding / low-density lipoprotein particle binding / negative regulation of mononuclear cell proliferation / vasoconstriction / choline binding / low-density lipoprotein particle receptor binding / Classical antibody-mediated complement activation / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more