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

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Basic information

Entry
Database: PDB / ID: 2xrb
TitleStructure of the N-terminal four domains of the complement regulator Rat Crry
ComponentsCOMPLEMENT REGULATORY PROTEIN CRRY
KeywordsIMMUNE SYSTEM / IMMUNOLOGY
Function / homology
Function and homology information


Regulation of Complement cascade / negative regulation of complement activation / negative regulation of complement activation, classical pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / T cell mediated immunity / complement activation / Neutrophil degranulation / complement activation, classical pathway / female pregnancy ...Regulation of Complement cascade / negative regulation of complement activation / negative regulation of complement activation, classical pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / T cell mediated immunity / complement activation / Neutrophil degranulation / complement activation, classical pathway / female pregnancy / cellular response to hypoxia / basolateral plasma membrane / in utero embryonic development / receptor complex / external side of plasma membrane / innate immune response / 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: 2.5 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 13, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references / Refinement description / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: COMPLEMENT REGULATORY PROTEIN CRRY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,02017
Polymers31,9251
Non-polymers1,09516
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)21.770, 105.339, 152.281
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 60.5 % / Description: NONE
Crystal growpH: 4.6
Details: 0.2 M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.6, 30% W/V PEGMME 2000.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 13105 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 45.42 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.8
Reflection shellResolution: 2.41→2.47 Å / Redundancy: 5 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.5 / % possible all: 97.9

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Processing

Software
NameVersionClassification
BUSTER2.9.5refinement
xia2USING XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DOMAINS FROM PDB ENTRIES 1OK9 AND 1GKN

1ok9

1gkn


Resolution: 2.5→29.26 Å / Cor.coef. Fo:Fc: 0.9221 / Cor.coef. Fo:Fc free: 0.8712 / SU R Cruickshank DPI: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.389 / SU Rfree Blow DPI: 0.251 / SU Rfree Cruickshank DPI: 0.24
RfactorNum. reflection% reflectionSelection details
Rfree0.237 651 5 %RANDOM
Rwork0.1847 ---
obs0.1872 13030 99.95 %-
Displacement parametersBiso mean: 32.65 Å2
Baniso -1Baniso -2Baniso -3
1-8.8592 Å20 Å20 Å2
2---3.8529 Å20 Å2
3----5.0063 Å2
Refine analyzeLuzzati coordinate error obs: 0.274 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 67 125 2158
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012080HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.172816HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d683SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes291HARMONIC5
X-RAY DIFFRACTIONt_it2080HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion18.73
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion270SEMIHARMONIC5
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_contact2363SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.7 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2652 125 4.72 %
Rwork0.2001 2521 -
all0.2032 2646 -
obs--99.95 %

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