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- PDB-4kkd: The X-ray crystal structure of Mannose-binding lectin-associated ... -

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Basic information

Entry
Database: PDB / ID: 4kkd
TitleThe X-ray crystal structure of Mannose-binding lectin-associated serine proteinase-3 reveals the structural basis for enzyme inactivity associated with the 3MC syndrome
ComponentsMannan-binding lectin serine protease 1
KeywordsHYDROLASE / protease / chymotrypsin fold / secreted
Function / homology
Function and homology information


Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / negative regulation of complement activation / complement activation, lectin pathway / zymogen activation / Scavenging by Class A Receptors / Initial triggering of complement / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / calcium-dependent protein binding / peptidase activity ...Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / negative regulation of complement activation / complement activation, lectin pathway / zymogen activation / Scavenging by Class A Receptors / Initial triggering of complement / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity / calcium ion binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / extracellular space / extracellular region / nucleoplasm / identical protein binding / cytosol
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 / 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 / EGF-like domain signature 2. / EGF-like domain / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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
IMIDAZOLE / Mannan-binding lectin serine protease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5991 Å
AuthorsYongqing, T. / Wilmann, P.G. / Reeve, S.B. / Coetzer, T.H. / Smith, A.I. / Whisstock, J.C. / Pike, R.N. / Wijeyewickrema, L.C.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The X-ray Crystal Structure of Mannose-binding Lectin-associated Serine Proteinase-3 Reveals the Structural Basis for Enzyme Inactivity Associated with the Carnevale, Mingarelli, Malpuech, and ...Title: The X-ray Crystal Structure of Mannose-binding Lectin-associated Serine Proteinase-3 Reveals the Structural Basis for Enzyme Inactivity Associated with the Carnevale, Mingarelli, Malpuech, and Michels (3MC) Syndrome.
Authors: Yongqing, T. / Wilmann, P.G. / Reeve, S.B. / Coetzer, T.H. / Smith, A.I. / Whisstock, J.C. / Pike, R.N. / Wijeyewickrema, L.C.
History
DepositionMay 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Structure summary
Revision 1.2Aug 21, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Mannan-binding lectin serine protease 1
B: Mannan-binding lectin serine protease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0843
Polymers96,0152
Non-polymers691
Water3,621201
1
A: Mannan-binding lectin serine protease 1


Theoretical massNumber of molelcules
Total (without water)48,0071
Polymers48,0071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mannan-binding lectin serine protease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0762
Polymers48,0071
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.840, 292.916, 43.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-997-

HOH

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Components

#1: Protein Mannan-binding lectin serine protease 1 / Complement factor MASP-3 / Complement-activating component of Ra-reactive factor / Mannose-binding ...Complement factor MASP-3 / Complement-activating component of Ra-reactive factor / Mannose-binding lectin-associated serine protease 1 / MASP-1 / Mannose-binding protein-associated serine protease / Ra-reactive factor serine protease p100 / RaRF / Serine protease 5 / Mannan-binding lectin serine protease 1 heavy chain / Mannan-binding lectin serine protease 1 light chain


Mass: 48007.309 Da / Num. of mol.: 2 / Mutation: K448Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRARF, CRARF1, MASP1, PRSS5 / Production host: Escherichia coli (E. coli)
References: UniProt: P48740, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.12 M NaCl, 18% (w/v) polyethylene glycol 4000 and 0.1 M imidazole pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.969 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 22, 2013
RadiationMonochromator: monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.599→48.82 Å / Num. all: 29907 / Num. obs: 29907 / % possible obs: 99.9 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 1.35
Reflection shellResolution: 2.599→2.71 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3562 / Rsym value: 0.786 / % possible all: 99.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
Auto-Rickshawphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
pointlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5991→48.819 Å / SU ML: 0.36 / Phase error: 24.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 1034 3.47 %random
Rwork0.194 ---
all0.1963 29830 --
obs0.1963 29830 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5991→48.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6197 0 5 201 6403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096377
X-RAY DIFFRACTIONf_angle_d1.2198666
X-RAY DIFFRACTIONf_dihedral_angle_d17.3432311
X-RAY DIFFRACTIONf_chiral_restr0.079950
X-RAY DIFFRACTIONf_plane_restr0.0061119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5991-2.73620.31441490.244028X-RAY DIFFRACTION99
2.7362-2.90760.35321630.24344033X-RAY DIFFRACTION100
2.9076-3.1320.2981350.23644041X-RAY DIFFRACTION100
3.132-3.44720.29231490.21024050X-RAY DIFFRACTION100
3.4472-3.94580.23021290.18014122X-RAY DIFFRACTION100
3.9458-4.97050.21241510.15894156X-RAY DIFFRACTION100
4.9705-48.82790.241580.17884366X-RAY DIFFRACTION100

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