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- PDB-1md8: Monomeric structure of the active catalytic domain of complement ... -

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Basic information

Entry
Database: PDB / ID: 1md8
TitleMonomeric structure of the active catalytic domain of complement protease C1r
ComponentsC1R COMPLEMENT SERINE PROTEASE
KeywordsHYDROLASE / complement / innate immunity / serine protease / activation / substrate specificity
Function / homology
Function and homology information


complement subcomponent C_overbar_1r_ / molecular sequestering activity / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / serine-type peptidase activity / complement activation, classical pathway / Regulation of Complement cascade / blood microparticle / immune response ...complement subcomponent C_overbar_1r_ / molecular sequestering activity / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / serine-type peptidase activity / complement activation, classical pathway / Regulation of Complement cascade / blood microparticle / immune response / serine-type endopeptidase activity / innate immune response / calcium ion binding / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Peptidase S1A, complement C1r/C1S/mannan-binding / Complement Module, domain 1 / Complement Module; domain 1 / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) ...Peptidase S1A, complement C1r/C1S/mannan-binding / Complement Module, domain 1 / Complement Module; domain 1 / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / 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 / Coagulation Factor Xa inhibitory site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Complement C1r subcomponent
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBudayova-Spano, M. / Grabarse, W. / Thielens, N.M. / Hillen, H. / Lacroix, M. / Schmidt, M. / Fontecilla-Camps, J. / Arlaud, G.J. / Gaboriaud, C.
CitationJournal: Structure / Year: 2002
Title: Monomeric structures of the zymogen and active catalytic domain of complement protease c1r: further insights into the c1 activation mechanism
Authors: Budayova-Spano, M. / Grabarse, W. / Thielens, N.M. / Hillen, H. / Lacroix, M. / Schmidt, M. / Fontecilla-Camps, J. / Arlaud, G.J. / Gaboriaud, C.
History
DepositionAug 7, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C1R COMPLEMENT SERINE PROTEASE


Theoretical massNumber of molelcules
Total (without water)37,1991
Polymers37,1991
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.911, 49.459, 77.249
Angle α, β, γ (deg.)90.00, 106.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1077-

HOH

DetailsThe biological assembly is a monomer

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Components

#1: Protein C1R COMPLEMENT SERINE PROTEASE / Complement C1r component


Mass: 37199.027 Da / Num. of mol.: 1 / Fragment: C-terminal CCP-SP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): High FiveTM / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P00736, complement subcomponent C_overbar_1r_
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: ammonium sulfate, TAPS, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112-20 %PEG60001reservoir
2100 mMHEPES1reservoirpH7.5
320 %glycerol1reservoiror 5% PEG4000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979549 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 9, 2001 / Details: mirrors
RadiationMonochromator: Monochromator can use either 111 or 311 Silicon single cristals.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979549 Å / Relative weight: 1
ReflectionResolution: 2.8→99 Å / Num. obs: 10075 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 92.4 Å2 / Rsym value: 0.065 / Net I/σ(I): 7
Reflection shellResolution: 2.8→2.87 Å / Rsym value: 0.189 / % possible all: 99.9
Reflection
*PLUS
Num. obs: 25998 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.189

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→12 Å / Rfactor Rfree error: 0.012 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 543 5.4 %RANDOM
Rwork0.198 ---
all0.2035 ---
obs0.2035 10075 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.0057 Å2 / ksol: 0.339214 e/Å3
Displacement parametersBiso mean: 49.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.39 Å20 Å20 Å2
2--10.71 Å20 Å2
3----7.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.8→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 0 82 2576
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it5.081.5
X-RAY DIFFRACTIONc_mcangle_it8.12
X-RAY DIFFRACTIONc_scbond_it7.12
X-RAY DIFFRACTIONc_scangle_it10.352.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 103 6.2 %
Rwork0.294 1570 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / Num. reflection obs: 10191 / Rfactor Rfree: 0.2545 / Rfactor Rwork: 0.2097
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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