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

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Basic information

Entry
Database: PDB / ID: 3pod
TitleCrystal structure of MBL collagen-like peptide
ComponentsMBL collagen-like peptide
KeywordsUNKNOWN FUNCTION / Collagen peptide / complement proteins / lectin pathway of complement / MASP-1 CUB1 and CUB2 domains / Bloodstream
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.497 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 22, 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

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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)6,6373
Polymers6,6373
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-25 kcal/mol
Surface area4250 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)13,2756
Polymers13,2756
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11910 Å2
ΔGint-71 kcal/mol
Surface area6410 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)13,2756
Polymers13,2756
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area11470 Å2
ΔGint-68 kcal/mol
Surface area6860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.880, 23.440, 25.800
Angle α, β, γ (deg.)90.00, 94.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide MBL collagen-like peptide


Mass: 2212.419 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: peptide
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 1.93 Å3/Da / Density % sol: 36.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.6M ammonium sulfate, 100mM MES buffer, 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: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.497→50 Å / Num. all: 8301 / Num. obs: 8299 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.98 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 25.94
Reflection shellResolution: 1.497→1.59 Å / Redundancy: 2.95 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 10.15 / Num. unique all: 1300 / % possible all: 96.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CAG

1cag


Resolution: 1.497→22.71 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.312 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19179 415 5 %RANDOM
Rwork0.115 ---
all0.11857 8301 --
obs0.11857 7884 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.125 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-0.36 Å2
2--0.47 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.497→22.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms473 0 0 94 567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021510
X-RAY DIFFRACTIONr_bond_other_d0.0030.02390
X-RAY DIFFRACTIONr_angle_refined_deg2.6532.503735
X-RAY DIFFRACTIONr_angle_other_deg1.2973933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.031569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.221518
X-RAY DIFFRACTIONr_chiral_restr0.1910.272
X-RAY DIFFRACTIONr_gen_planes_refined0.010.03525
X-RAY DIFFRACTIONr_gen_planes_other00.0227
X-RAY DIFFRACTIONr_mcbond_it2.1821.5384
X-RAY DIFFRACTIONr_mcbond_other0.8471.5126
X-RAY DIFFRACTIONr_mcangle_it3.1542633
X-RAY DIFFRACTIONr_scbond_it4.4753126
X-RAY DIFFRACTIONr_scangle_it6.4114.5102
X-RAY DIFFRACTIONr_rigid_bond_restr1.8353897
LS refinement shellResolution: 1.497→1.535 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 29 -
Rwork0.14 549 -
obs--100 %

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