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- PDB-1lj7: Crystal structure of calcium-depleted human C-reactive protein fr... -

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Basic information

Entry
Database: PDB / ID: 1lj7
TitleCrystal structure of calcium-depleted human C-reactive protein from perfectly twinned data
ComponentsC-reactive protein
KeywordsUNKNOWN FUNCTION / pentraxin fold / pentamer / decamer / twinned
Function / homology
Function and homology information


regulation of interleukin-8 production / opsonization / complement component C1q complex binding / negative regulation of mononuclear cell proliferation / low-density lipoprotein particle binding / 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 / negative regulation of mononuclear cell proliferation / low-density lipoprotein particle binding / 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 ...: / 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: 3.15 Å
AuthorsRamadan, M.A. / Shrive, A.K. / Holden, D. / Myles, D.A. / Volanakis, J.E. / DeLucas, L.J. / Greenhough, T.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The three-dimensional structure of calcium-depleted human C-reactive protein from perfectly twinned crystals.
Authors: Ramadan, M.A. / Shrive, A.K. / Holden, D. / Myles, D.A. / Volanakis, J.E. / DeLucas, L.J. / Greenhough, T.J.
History
DepositionApr 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 11 A few small regions of the structure are not well defined due to the twinning and asociated ... A few small regions of the structure are not well defined due to the twinning and asociated disorder. The twinning 2-fold is parallel to the 2-fold ncs operator relating the two pentamers in the assymetric unit. Removal of calcium results in residues in the calcium- binding loop 140-150 becoming disordered and mobile. The loops and parts of loops that are visible are held in place by crystal contacts
Remark 300 Biomolecule: 1,2 This entry contains the crystallographic assymetric unit which consists of 10 ... Biomolecule: 1,2 This entry contains the crystallographic assymetric unit which consists of 10 chain(s). See remark 350 for information on generating the biological molecule(s). It is, however, not clear whether the biomolecule consists of one or two pentameters

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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


Theoretical massNumber of molelcules
Total (without water)230,68010
Polymers230,68010
Non-polymers00
Water00
1
A: C-reactive protein
B: C-reactive protein
C: C-reactive protein
D: C-reactive protein
E: C-reactive protein


Theoretical massNumber of molelcules
Total (without water)115,3405
Polymers115,3405
Non-polymers00
Water0
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


Theoretical massNumber of molelcules
Total (without water)115,3405
Polymers115,3405
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.310, 102.310, 309.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
C-reactive protein


Mass: 23068.039 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Details: purified from serum / Source: (natural) Homo sapiens (human) / References: UniProt: P02741
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 17

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 66 %
Description: Data in this section (200) refers to the twinned space group P4(1)22
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Details: DeLucas, L.J., (1987) J. Mol. Biol., 196, 741.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 Å
DetectorType: CEA / Detector: FILM / Date: Jan 1, 1989
RadiationMonochromator: Germanium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 3.15→72.6 Å / Num. obs: 26903 / % possible obs: 92.1 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 5.4
Reflection shellResolution: 3.15→3.25 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2.4 / % possible all: 55.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
CCP4model building
X-PLOR3.851refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Amended pentamer from PDB ENTRY 1GNH

1gnh


Resolution: 3.15→20 Å / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Non-standard refinement, including deconvolution, carried out in P43 (See Ramadan et al). The completeness in P43 is significantly less than in P422 (See experimental details) due to the ...Details: Non-standard refinement, including deconvolution, carried out in P43 (See Ramadan et al). The completeness in P43 is significantly less than in P422 (See experimental details) due to the deconvolution procedure. Data was merged in P4 (1)22. In experimental details, refer to this space group rather than P43. Refinement carried out in P43
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2072 5 %Random
Rwork0.186 ---
obs-38645 81.2 %-
Displacement parametersBiso mean: 20.8 Å2
Refinement stepCycle: LAST / Resolution: 3.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15996 0 0 0 15996
LS refinement shellResolution: 3.15→3.29 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.26 147
Rwork0.231 2645
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.231

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