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- PDB-2xrd: Structure of the N-terminal four domains of the complement regula... -

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Basic information

Entry
Database: PDB / ID: 2xrd
TitleStructure of the N-terminal four domains of the complement regulator Rat Crry
ComponentsCOMPLEMENT REGULATORY PROTEIN CRRY
KeywordsIMMUNE SYSTEM / EXTRACELLULAR PROTEIN / SUSHI (CCP/SCR) DOMAINS
Function / homology
Function and homology information


Regulation of Complement cascade / negative regulation of complement activation, classical pathway / negative regulation of complement activation / T cell mediated immunity / regulation of complement-dependent cytotoxicity / regulation of complement activation / complement activation / Neutrophil degranulation / complement activation, classical pathway / female pregnancy ...Regulation of Complement cascade / negative regulation of complement activation, classical pathway / negative regulation of complement activation / T cell mediated immunity / regulation of complement-dependent cytotoxicity / regulation of complement activation / complement activation / Neutrophil degranulation / complement activation, classical pathway / female pregnancy / basolateral plasma membrane / cellular response to hypoxia / in utero embryonic development / receptor complex / innate immune response / external side of plasma membrane / cell surface / extracellular space / plasma membrane
Similarity search - Function
: / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Complement component receptor 1-like protein
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsLeath, K.J. / Roversi, P. / Johnson, S. / Morgan, B.P. / Lea, S.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structures of the Rat Complement Regulator Crry.
Authors: Roversi, P. / Johnson, S. / Caesar, J.J.E. / Mclean, F. / Leath, K.J. / Tsiftsoglou, S.A. / Morgan, B.P. / Harris, C.L. / Sim, R.B. / Lea, S.M.
History
DepositionSep 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references / Other ...Database references / Other / Refinement description / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COMPLEMENT REGULATORY PROTEIN CRRY


Theoretical massNumber of molelcules
Total (without water)31,9251
Polymers31,9251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)205.840, 100.370, 21.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein COMPLEMENT REGULATORY PROTEIN CRRY / CRRY / ANTIGEN 5I2


Mass: 31925.393 Da / Num. of mol.: 1
Fragment: EXTRACELLULAR N-TERMINAL FOUR CCP DOMAINS, RESIDUES 1-288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PET SERIES / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q63135
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: 3.55 Å3/Da / Density % sol: 70.3 % / Description: NONE
Crystal growpH: 4.6
Details: 0.1 M SODIUM ACETATE PH 4.6, 2.0 M SODIUM CHLORIDE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.3→38 Å / Num. obs: 7742 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 43.44 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 8
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / % possible all: 98.5

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Processing

Software
NameVersionClassification
BUSTER2.9.5refinement
XIAUSING XDSdata reduction
XIAUSING SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1OK9 AND 1GKN

1ok9

1gkn


Resolution: 3.5→38.09 Å / Cor.coef. Fo:Fc: 0.7016 / Cor.coef. Fo:Fc free: 0.759 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.492
RfactorNum. reflection% reflectionSelection details
Rfree0.2509 288 4.5 %RANDOM
Rwork0.2498 ---
obs0.2498 6390 99.81 %-
Displacement parametersBiso mean: 68.07 Å2
Baniso -1Baniso -2Baniso -3
1-5.9682 Å20 Å20 Å2
2---25.0723 Å20 Å2
3---19.1041 Å2
Refine analyzeLuzzati coordinate error obs: 0.802 Å
Refinement stepCycle: LAST / Resolution: 3.5→38.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1918 0 0 0 1918
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d1978HARMONIC2
X-RAY DIFFRACTIONt_angle_deg2697HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d648SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes48HARMONIC2
X-RAY DIFFRACTIONt_gen_planes281HARMONIC5
X-RAY DIFFRACTIONt_it1978HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion263SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2124SEMIHARMONIC4
LS refinement shellResolution: 3.5→3.91 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2379 75 4.3 %
Rwork0.2589 1670 -
all0.2581 1745 -
obs--99.81 %

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