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- PDB-1szb: Crystal structure of the human MBL-associated protein 19 (MAp19) -

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Basic information

Entry
Database: PDB / ID: 1szb
TitleCrystal structure of the human MBL-associated protein 19 (MAp19)
Componentsmannose binding lectin-associated serine protease-2 related protein, MAp19 (19kDa)
KeywordsPROTEIN BINDING / CALCIUM / COMPLEMENT / INNATE IMMUNITY / CUB / EGF
Function / homology
Function and homology information


mannan-binding lectin-associated serine protease-2 / complement component C4b binding / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / complement activation, lectin pathway / Initial triggering of complement / complement activation, classical pathway / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity ...mannan-binding lectin-associated serine protease-2 / complement component C4b binding / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / complement activation, lectin pathway / Initial triggering of complement / complement activation, classical pathway / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity / calcium ion binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding
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/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation 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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGregory, L.A. / Thielens, N.M. / Arlaud, G.J. / Fontecilla-Camps, J.C. / Gaboriaud, C.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The X-ray structure of human MBL-associated protein 19 (MAp19) and its interaction site with mannan-binding lectin and L-ficolin
Authors: Gregory, L.A. / Thielens, N.M. / Matsushita, M. / Sorensen, R. / Arlaud, G.J. / Fontecilla-Camps, J.C. / Gaboriaud, C.
History
DepositionApr 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_dist_value / _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_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_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: mannose binding lectin-associated serine protease-2 related protein, MAp19 (19kDa)
B: mannose binding lectin-associated serine protease-2 related protein, MAp19 (19kDa)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3816
Polymers38,2202
Non-polymers1604
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-54 kcal/mol
Surface area18160 Å2
MethodPISA
2
A: mannose binding lectin-associated serine protease-2 related protein, MAp19 (19kDa)
B: mannose binding lectin-associated serine protease-2 related protein, MAp19 (19kDa)
hetero molecules

A: mannose binding lectin-associated serine protease-2 related protein, MAp19 (19kDa)
B: mannose binding lectin-associated serine protease-2 related protein, MAp19 (19kDa)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,76112
Polymers76,4414
Non-polymers3218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area6550 Å2
ΔGint-112 kcal/mol
Surface area35260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.754, 67.754, 187.923
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1058-

HOH

Detailshomodimer, as observed in the asymetric unit

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Components

#1: Protein mannose binding lectin-associated serine protease-2 related protein, MAp19 (19kDa)


Mass: 19110.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MASP2 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): HIGH FIVE INSECT CELLS / References: UniProt: O00187
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.838 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.946 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 21, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.946 Å / Relative weight: 1
ReflectionResolution: 2.5→17 Å / Num. obs: 15712 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.047 / Net I/σ(I): 23.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 1489 / Rsym value: 0.357 / % possible all: 86.1

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NT0

1nt0


Resolution: 2.5→17 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.316 1579 RANDOM
Rwork0.261 --
obs0.263 15692 -
all-15692 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--16.037 Å20 Å20 Å2
2---16.037 Å20 Å2
3---32.075 Å2
Refinement stepCycle: LAST / Resolution: 2.5→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2641 0 4 144 2789

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