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- PDB-3pon: Crystal structure of MBL collagen-like peptide -

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Basic information

Entry
Database: PDB / ID: 3pon
TitleCrystal structure of MBL collagen-like peptide
ComponentsMBL collagen-like peptide
KeywordsUNKNOWN FUNCTION / Collagen peptide / MBL collagen-like region / Complement protein / lectin pathway of complement / MASPs (MASP-1 to 3) CUB1 and CUB2 domains / Bloodstream
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGingras, A.R. / Moody, P.C.E. / Wallis, R.
CitationJournal: Structure / Year: 2011
Title: Structural Basis of Mannan-Binding Lectin Recognition by Its Associated Serine Protease MASP-1: Implications for Complement Activation.
Authors: Gingras, A.R. / Girija, U.V. / Keeble, A.H. / Panchal, R. / Mitchell, D.A. / Moody, P.C. / Wallis, R.
History
DepositionNov 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Sep 6, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MBL collagen-like peptide
B: MBL collagen-like peptide
C: MBL collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)7,4393
Polymers7,4393
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-26 kcal/mol
Surface area4560 Å2
MethodPISA
2
A: MBL collagen-like peptide
B: MBL collagen-like peptide
C: MBL collagen-like peptide

A: MBL collagen-like peptide
B: MBL collagen-like peptide
C: MBL collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)14,8786
Polymers14,8786
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13200 Å2
ΔGint-72 kcal/mol
Surface area6750 Å2
MethodPISA
3
A: MBL collagen-like peptide
B: MBL collagen-like peptide
C: MBL collagen-like peptide

A: MBL collagen-like peptide
B: MBL collagen-like peptide
C: MBL collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)14,8786
Polymers14,8786
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area12530 Å2
ΔGint-66 kcal/mol
Surface area7410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.270, 23.650, 26.940
Angle α, β, γ (deg.)90.00, 94.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-46-

HOH

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Components

#1: Protein/peptide MBL collagen-like peptide


Mass: 2479.700 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Synthetic peptide
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 1.82 Å3/Da / Density % sol: 32.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.6M Ammonium Sulphate, 100mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2010 / Details: focusing mirrors
RadiationMonochromator: horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.5→23.485 Å / Num. obs: 8744 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2 / Num. unique all: 3561 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3POD

3pod


Resolution: 1.5→21.26 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.707 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18981 415 4.8 %RANDOM
Rwork0.14097 ---
all0.14344 ---
obs0.14344 8296 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20.03 Å2
2--0.38 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.5→21.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms515 0 0 98 613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.021556
X-RAY DIFFRACTIONr_bond_other_d0.0160.02425
X-RAY DIFFRACTIONr_angle_refined_deg2.7772.501802
X-RAY DIFFRACTIONr_angle_other_deg1.20531016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.693576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg31.1941518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1530.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.03578
X-RAY DIFFRACTIONr_gen_planes_other00.0230
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3231.5420
X-RAY DIFFRACTIONr_mcbond_other0.8991.5139
X-RAY DIFFRACTIONr_mcangle_it3.3452692
X-RAY DIFFRACTIONr_scbond_it5.0843136
X-RAY DIFFRACTIONr_scangle_it7.1134.5110
X-RAY DIFFRACTIONr_rigid_bond_restr2.1923978
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 21 -
Rwork0.209 600 -
obs--98.89 %

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