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- PDB-1bv4: APO-MANNOSE-BINDING PROTEIN-C -

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Basic information

Entry
Database: PDB / ID: 1bv4
TitleAPO-MANNOSE-BINDING PROTEIN-C
ComponentsPROTEIN (MANNOSE-BINDING PROTEIN-C)
KeywordsSUGAR BINDING PROTEIN / C-TYPE LECTIN / CALCIUM-BINDING PROTEIN / COLLECTIN
Function / homology
Function and homology information


Lectin pathway of complement activation / Initial triggering of complement / positive regulation of opsonization / complement activation, lectin pathway / positive regulation of complement activation / negative regulation of viral process / galactose binding / killing by host of symbiont cells / positive regulation of protein processing / cell surface pattern recognition receptor signaling pathway ...Lectin pathway of complement activation / Initial triggering of complement / positive regulation of opsonization / complement activation, lectin pathway / positive regulation of complement activation / negative regulation of viral process / galactose binding / killing by host of symbiont cells / positive regulation of protein processing / cell surface pattern recognition receptor signaling pathway / collagen trimer / serine-type endopeptidase complex / surfactant homeostasis / phosphatidylinositol-4-phosphate binding / D-mannose binding / complement activation, classical pathway / multivesicular body / antiviral innate immune response / positive regulation of phagocytosis / calcium-dependent protein binding / protease binding / defense response to Gram-positive bacterium / signaling receptor binding / innate immune response / calcium ion binding / protein-containing complex / proteolysis / extracellular space / identical protein binding
Similarity search - Function
Collectin, C-type lectin-like domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. ...Collectin, C-type lectin-like domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Mannose-binding protein C
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNg, K.K.-S. / Weis, W.I.
CitationJournal: Biochemistry / Year: 1998
Title: Ca2+-dependent structural changes in C-type mannose-binding proteins.
Authors: Ng, K.K. / Park-Snyder, S. / Weis, W.I.
History
DepositionSep 22, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (MANNOSE-BINDING PROTEIN-C)
B: PROTEIN (MANNOSE-BINDING PROTEIN-C)
C: PROTEIN (MANNOSE-BINDING PROTEIN-C)
D: PROTEIN (MANNOSE-BINDING PROTEIN-C)


Theoretical massNumber of molelcules
Total (without water)52,6464
Polymers52,6464
Non-polymers00
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.390, 132.620, 46.810
Angle α, β, γ (deg.)90.00, 94.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.3982, -0.7381, 0.5446), (-0.7206, -0.6191, -0.3121), (0.5675, -0.2682, -0.7784)19.405, 9.061, -37.047
2given(0.9653, 0.2159, 0.1468), (0.2196, -0.9755, -0.0091), (0.1413, 0.041, -0.9891)0.56, 22.051, -26
3given(0.3635, -0.8525, 0.3757), (0.7764, 0.5001, 0.3836), (-0.5149, 0.1523, 0.8436)15.07, 18.324, 13.243

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Components

#1: Protein
PROTEIN (MANNOSE-BINDING PROTEIN-C)


Mass: 13161.604 Da / Num. of mol.: 4 / Fragment: SUBTILISIN FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Plasmid: PINOMPAII / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JA221 / References: UniProt: P08661
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 36 %
Crystal growpH: 6.2
Details: 12% PEG 8000, 100 MM NAMES, PH 6.1, 200 MM LICL, 2 MM EDTA 0.02%, NAN3, pH 6.2
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
28-12 %(w/v)PEG80001reservoir
3100 mMTris-Cl1reservoirpH8.0
410 mM1reservoirNaCl
50.02 %1reservoirNaN3
60.375 mM1reservoirDyCl3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 33667 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.6
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 6.2 / % possible all: 99.8
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.26

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNS0.3Crefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RDO

1rdo


Resolution: 1.85→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3287 10 %RANDOM
Rwork0.212 ---
obs0.212 33070 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.1 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20.38 Å2
2---3.65 Å20 Å2
3---2.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Luzzati d res low-50 Å
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3237 0 0 234 3471
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.41.5
X-RAY DIFFRACTIONc_mcangle_it3.392
X-RAY DIFFRACTIONc_scbond_it3.732
X-RAY DIFFRACTIONc_scangle_it5.182.5
LS refinement shellResolution: 1.85→1.92 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.304 290 10 %
Rwork0.237 2895 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Software
*PLUS
Name: CNS / Version: 0.3C / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.304 / % reflection Rfree: 10 % / Rfactor Rwork: 0.237 / Rfactor obs: 0.237

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