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- PDB-1buu: ONE HO3+ FORM OF RAT MANNOSE-BINDING PROTEIN A -

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Basic information

Entry
Database: PDB / ID: 1buu
TitleONE HO3+ FORM OF RAT MANNOSE-BINDING PROTEIN A
ComponentsPROTEIN (MANNOSE-BINDING PROTEIN A)
KeywordsSUGAR BINDING PROTEIN / LECTIN / HOST DEFENSE / METALLOPROTEIN
Function / homology
Function and homology information


calcium-dependent carbohydrate binding / complement activation, lectin pathway / oligosaccharide binding / killing by host of symbiont cells / collagen trimer / surfactant homeostasis / phosphatidylinositol-4-phosphate binding / protein homotrimerization / D-mannose binding / polysaccharide binding ...calcium-dependent carbohydrate binding / complement activation, lectin pathway / oligosaccharide binding / killing by host of symbiont cells / collagen trimer / surfactant homeostasis / phosphatidylinositol-4-phosphate binding / protein homotrimerization / D-mannose binding / polysaccharide binding / complement activation, classical pathway / multivesicular body / positive regulation of phagocytosis / calcium-dependent protein binding / protease binding / defense response to Gram-positive bacterium / calcium ion binding / protein homodimerization activity / 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
HOLMIUM ATOM / Mannose-binding protein A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNg, K.K.-S. / Park-Snyder, 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 6, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 9, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (MANNOSE-BINDING PROTEIN A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6152
Polymers18,4501
Non-polymers1651
Water3,081171
1
A: PROTEIN (MANNOSE-BINDING PROTEIN A)
hetero molecules

A: PROTEIN (MANNOSE-BINDING PROTEIN A)
hetero molecules

A: PROTEIN (MANNOSE-BINDING PROTEIN A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8446
Polymers55,3493
Non-polymers4953
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+3/2,-x+1,y+1/21
crystal symmetry operation10_646-y+1,z-1/2,-x+3/21
2
A: PROTEIN (MANNOSE-BINDING PROTEIN A)
hetero molecules

A: PROTEIN (MANNOSE-BINDING PROTEIN A)
hetero molecules

A: PROTEIN (MANNOSE-BINDING PROTEIN A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8446
Polymers55,3493
Non-polymers4953
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_546z,x-1,y+11
crystal symmetry operation9_645y+1,z-1,x1
Buried area6480 Å2
ΔGint-87 kcal/mol
Surface area21350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.400, 94.400, 94.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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


Mass: 18449.816 Da / Num. of mol.: 1
Fragment: LECTIN, TRIMERIZATION, AND PORTION OF COLLAGENOUS DOMAIN DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Plasmid: PINIIIOMPA2 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P19999
#2: Chemical ChemComp-HO / HOLMIUM ATOM


Mass: 164.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ho
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FIRST 4 RESIDUES IN THE EXPRESSION CONSTRUCT, ALA-ILE-GLU-VAL, ARE A CLONING ARTIFACT AND ARE ...THE FIRST 4 RESIDUES IN THE EXPRESSION CONSTRUCT, ALA-ILE-GLU-VAL, ARE A CLONING ARTIFACT AND ARE NOT PART OF THE NATIVE SEQUENCE.

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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: 3.8 Å3/Da / Density % sol: 67 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: HANGING-DROP VAPOR DIFFUSION AGAINST RESERVOIR CONTAINING 11-15% (W/V) PEG 3350, 0.325 MM HOCL3, 100 MM TRIS-CL PH 8.0, 10 MM NACL, 0.02% NAN3., vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 15, 1994 / Details: 0.3 MM COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 20530 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.215 / Rsym value: 0.215 / % possible all: 88
Reflection shell
*PLUS
% possible obs: 88 %

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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: PDB ENTRY 1RTM, CHAIN 1

1rtm


Resolution: 1.9→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 1000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: MLF TARGET USED. THE FIRST 19 RESIDUES OF THE EXPRESSION CONSTRUCT, CONTAINING SEQUENCE FROM THE COLLAGENOUS DOMAIN, ARE DISORDERED AND CANNOT BE DISTINGUISHED IN ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2020 9 %RANDOM
Rwork0.198 ---
obs0.198 20530 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80.9 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 28.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1153 0 1 171 1325
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.22.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.271 125 5.7 %
Rwork0.233 1104 -
obs--56.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3C / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scangle_it3.22.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.271 / % reflection Rfree: 5.7 % / Rfactor Rwork: 0.233 / Rfactor obs: 0.233

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