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- PDB-1nt0: Crystal structure of the CUB1-EGF-CUB2 region of MASP2 -

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Basic information

Entry
Database: PDB / ID: 1nt0
TitleCrystal structure of the CUB1-EGF-CUB2 region of MASP2
Componentsmannose-binding protein associated serine protease-2
KeywordsHYDROLASE / SUGAR BINDING PROTEIN / mannose-binding protein / MASP / CUB domain / EGF like domain.
Function / homology
Function and homology information


mannan-binding lectin-associated serine protease-2 / Ficolins bind to repetitive carbohydrate structures on the target cell surface / complement component C4b binding / Lectin pathway of complement activation / Initial triggering of complement / complement activation, lectin pathway / complement activation / complement activation, classical pathway / calcium-dependent protein binding / peptidase activity ...mannan-binding lectin-associated serine protease-2 / Ficolins bind to repetitive carbohydrate structures on the target cell surface / complement component C4b binding / Lectin pathway of complement activation / Initial triggering of complement / complement activation, lectin pathway / complement activation / complement activation, classical pathway / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space
Similarity search - Function
Spermadhesin, CUB domain / Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Calcium-binding EGF domain / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) ...Spermadhesin, CUB domain / Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Calcium-binding EGF domain / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Laminin / Laminin / 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. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Jelly Rolls / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mannan-binding lectin serine protease 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.7 Å
AuthorsFeinberg, H. / Uitdehaag, J.C.M. / Davies, J.M. / Wallis, R. / Drickamer, K. / Weis, W.I.
CitationJournal: Embo J. / Year: 2003
Title: Crystal structure of the CUB1-EGF-CUB2 region of mannose-binding protein associated serine protease-2
Authors: Feinberg, H. / Uitdehaag, J.C.M. / Davies, J.M. / Wallis, R. / Drickamer, K. / Weis, W.I.
History
DepositionJan 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mannose-binding protein associated serine protease-2
G: mannose-binding protein associated serine protease-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7598
Polymers65,1122
Non-polymers6476
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-32 kcal/mol
Surface area27820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.411, 103.901, 70.484
Angle α, β, γ (deg.)90.00, 119.93, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsDimer. Strict NCS was used in refinement. Both protomers are included in the pdb file.

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Components

#1: Protein mannose-binding protein associated serine protease-2 / MASP2


Mass: 32556.035 Da / Num. of mol.: 2 / Fragment: CUB1-EGF-CUB2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Cricetulus griseus (Chinese hamster) / Tissue (production host): ovary cells / References: UniProt: Q9JJS8
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.79 Å3/Da / Density % sol: 67.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein: 2-5 mg/ml, 50 mM Tris pH=8.2, 10 mM CaCl2 and 0.5 M NaCl. Reservoir: 0.8-1.0 M Na2-Tartrate, 80 mM Li2SO4 and 0.1 MES pH=6.5, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12-5 mg/mlprotein1drop
250 mMTris1droppH8.2
310 mM1dropCaCl2
40.5 M1dropNaCl
50.8-1.0 Msodium tartrate1reservoir
680 mM1reservoirLi2SO4
70.1 MMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→39.56 Å / Num. all: 23987 / Num. obs: 23873 / % possible obs: 98.7 % / Observed criterion σ(I): -3.7
Reflection shellResolution: 2.7→2.77 Å / % possible all: 99.6
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 40 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
Highest resolution: 2.7 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.346

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.7→39.56 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2357 9.9 %RANDOM
Rwork0.248 ---
all-23873 --
obs-23873 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.2743 Å2 / ksol: 0.327709 e/Å3
Displacement parametersBiso mean: 44 Å2
Baniso -1Baniso -2Baniso -3
1--5.13 Å20 Å21.69 Å2
2---9.96 Å20 Å2
3---15.09 Å2
Refine analyzeLuzzati coordinate error free: 0.45 Å / Luzzati sigma a free: 0.48 Å
Refinement stepCycle: LAST / Resolution: 2.7→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4050 0 38 106 4194
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_d26.5
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.842
X-RAY DIFFRACTIONc_scbond_it5.312
X-RAY DIFFRACTIONc_scangle_it6.92.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 392 9.9 %
Rwork0.336 3585 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMEDO.TOP
X-RAY DIFFRACTION5EDO.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.282
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0069
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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