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- PDB-3l2y: The structure of C-reactive protein bound to phosphoethanolamine -

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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 / choline binding / vasoconstriction / 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 / choline binding / vasoconstriction / 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
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
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)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:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 1 - 206 / Label seq-ID: 1 - 206

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 1:206 )AA
2chain B and (resseq 1:206 )BB
3chain C and (resseq 1:206 )CC
4chain D and (resseq 1:206 )DD
5chain E and (resseq 1:206 )EE
6chain F and (resseq 1:206 )FF
7chain G and (resseq 1:206 )GG
8chain H and (resseq 1:206 )HH
9chain I and (resseq 1:206 )II
10chain J and (resseq 1:206 )JJ
11chain K and (resseq 1:206 )KK
12chain L and (resseq 1:206 )LL
13chain M and (resseq 1:206 )MM
14chain N and (resseq 1:206 )NN
15chain O and (resseq 1:206 )OO
16chain P and (resseq 1:206 )PP
17chain Q and (resseq 1:206 )QQ
18chain R and (resseq 1:206 )RR
19chain S and (resseq 1:206 )SS
20chain T and (resseq 1:206 )TT

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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
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: 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

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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

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Phasing

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

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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

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