[English] 日本語
Yorodumi
- PDB-3l2y: The structure of C-reactive protein bound to phosphoethanolamine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3l2y
TitleThe structure of C-reactive protein bound to phosphoethanolamine
ComponentsC-reactive protein
KeywordsCalcium-BINDING PROTEIN / PENTRAXIN / ACUTE PHASE REACTANT / IMMUNE SYSTEM / PHOSPHOETHANOLAMINE / Acute phase / Metal-binding / Pyrrolidone carboxylic acid / Secreted
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 / 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 / negative regulation of mononuclear cell proliferation / vasoconstriction / choline binding / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / C-reactive protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMikolajek, H. / Kolstoe, S.E. / Wood, S.P. / Pepys, M.B.
CitationJournal: J.Mol.Recognit. / Year: 2011
Title: Structural basis of ligand specificity in the human pentraxins, C-reactive protein and serum amyloid P component.
Authors: Mikolajek, H. / Kolstoe, S.E. / Pye, V.E. / Mangione, P. / Pepys, M.B. / Wood, S.P.
History
DepositionDec 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
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)465,78580
Polymers461,36120
Non-polymers4,42460
Water2,756153
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)116,44620
Polymers115,3405
Non-polymers1,10615
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-23 kcal/mol
Surface area40690 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)116,44620
Polymers115,3405
Non-polymers1,10615
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-23 kcal/mol
Surface area40700 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)116,44620
Polymers115,3405
Non-polymers1,10615
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-23 kcal/mol
Surface area40660 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)116,44620
Polymers115,3405
Non-polymers1,10615
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-23 kcal/mol
Surface area40730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)278.448, 278.448, 92.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171Q
181R
191S
201T

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 1:206 )A1 - 206
211chain B and (resseq 1:206 )B1 - 206
311chain C and (resseq 1:206 )C1 - 206
411chain D and (resseq 1:206 )D1 - 206
511chain E and (resseq 1:206 )E1 - 206
611chain F and (resseq 1:206 )F1 - 206
711chain G and (resseq 1:206 )G1 - 206
811chain H and (resseq 1:206 )H1 - 206
911chain I and (resseq 1:206 )I1 - 206
1011chain J and (resseq 1:206 )J1 - 206
1111chain K and (resseq 1:206 )K1 - 206
1211chain L and (resseq 1:206 )L1 - 206
1311chain M and (resseq 1:206 )M1 - 206
1411chain N and (resseq 1:206 )N1 - 206
1511chain O and (resseq 1:206 )O1 - 206
1611chain P and (resseq 1:206 )P1 - 206
1711chain Q and (resseq 1:206 )Q1 - 206
1811chain R and (resseq 1:206 )R1 - 206
1911chain S and (resseq 1:206 )S1 - 206
2011chain T and (resseq 1:206 )T1 - 206

-
Components

#1: Protein
C-reactive protein


Mass: 23068.039 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / 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-OPE / PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / COLAMINE PHOSPHORIC ACID


Mass: 141.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H8NO4P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.87 Å3/Da / Density % sol: 68.22 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.06M TRIS-HCL pH7.5, 10% MPD, 0.01M CaCl2, 0.14M NaCl, 0.1% NaN3, 0.1% LM AGAROSE, VAPOR DIFFUSION, HANGING DROP, temperature 285.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9686 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.7→125 Å / Num. all: 193026 / Num. obs: 193026 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 12.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 2 / Num. measured all: 139700 / Num. unique all: 27836 / Rsym value: 0.764 / % possible all: 98.9

-
Phasing

Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å124.53 Å
Translation2.7 Å124.53 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASER1.3.3phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→124.526 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.806 / SU ML: 0.44 / σ(F): 1.35 / Phase error: 25.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2462 9714 5.04 %
Rwork0.2236 --
obs0.2247 192736 99.27 %
all-192826 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.233 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 149.79 Å2 / Biso min: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.625 Å20 Å20 Å2
2---1.625 Å2-0 Å2
3---3.2499 Å2
Refinement stepCycle: LAST / Resolution: 2.7→124.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32640 0 200 153 32993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00933720
X-RAY DIFFRACTIONf_angle_d1.08245800
X-RAY DIFFRACTIONf_dihedral_angle_d14.47412060
X-RAY DIFFRACTIONf_chiral_restr0.0724940
X-RAY DIFFRACTIONf_plane_restr0.0055800
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1632X-RAY DIFFRACTIONPOSITIONAL
12B1632X-RAY DIFFRACTIONPOSITIONAL0.054
13C1632X-RAY DIFFRACTIONPOSITIONAL0.049
14D1632X-RAY DIFFRACTIONPOSITIONAL0.048
15E1632X-RAY DIFFRACTIONPOSITIONAL0.053
16F1632X-RAY DIFFRACTIONPOSITIONAL0.051
17G1632X-RAY DIFFRACTIONPOSITIONAL0.054
18H1632X-RAY DIFFRACTIONPOSITIONAL0.044
19I1632X-RAY DIFFRACTIONPOSITIONAL0.06
110J1632X-RAY DIFFRACTIONPOSITIONAL0.053
111K1632X-RAY DIFFRACTIONPOSITIONAL0.041
112L1632X-RAY DIFFRACTIONPOSITIONAL0.057
113M1632X-RAY DIFFRACTIONPOSITIONAL0.049
114N1632X-RAY DIFFRACTIONPOSITIONAL0.053
115O1632X-RAY DIFFRACTIONPOSITIONAL0.053
116P1632X-RAY DIFFRACTIONPOSITIONAL0.044
117Q1632X-RAY DIFFRACTIONPOSITIONAL0.065
118R1632X-RAY DIFFRACTIONPOSITIONAL0.053
119S1632X-RAY DIFFRACTIONPOSITIONAL0.053
120T1632X-RAY DIFFRACTIONPOSITIONAL0.059
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.73070.43013480.3813587097
2.7307-2.76280.38613360.3638597198
2.7628-2.79650.35033260.3349602899
2.7965-2.83190.37623160.3324602599
2.8319-2.86920.3423240.3162605699
2.8692-2.90850.31763070.3024603699
2.9085-2.95010.32213240.2995605299
2.9501-2.99410.32643170.2997605999
2.9941-3.04090.32263120.2948603999
3.0409-3.09070.32393150.2873606799
3.0907-3.1440.30943490.28599699
3.144-3.20120.30183380.2736609599
3.2012-3.26280.31442970.2725607699
3.2628-3.32940.29863400.2619605799
3.3294-3.40180.29712810.2631614199
3.4018-3.48090.28043380.2596606299
3.4809-3.5680.29963230.25866123100
3.568-3.66450.27073230.24646125100
3.6645-3.77230.26353320.2436056100
3.7723-3.89410.26243510.23926089100
3.8941-4.03330.21673000.226181100
4.0333-4.19480.22873100.19556162100
4.1948-4.38570.1852710.18316216100
4.3857-4.61690.17883560.16416118100
4.6169-4.90620.19123530.16126147100
4.9062-5.2850.18982900.17566211100
5.285-5.81680.19463250.1766195100
5.8168-6.65850.17793450.15926205100
6.6585-8.38880.17123340.14756264100
8.3888-124.65850.23913330.2296630098

+
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://pdbjlvh1.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