1YTT | pdb_00001ytt

YB SUBSTITUTED SUBTILISIN FRAGMENT OF MANNOSE BINDING PROTEIN-A (SUB-MBP-A), MAD STRUCTURE AT 110K

• PDB DOI: https://doi.org/10.2210/pdb1YTT/pdb

• Classification: MANNOSE-BINDING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1995-11-09 Released: 1996-06-10 
• Deposition Author(s): Burling, F.T., Weis, W.I., Flaherty, K.M., Brunger, A.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.206 (Depositor) 
• R-Value Work: 
  0.185 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Direct observation of protein solvation and discrete disorder with experimental crystallographic phases.

Burling, F.T., Weis, W.I., Flaherty, K.M., Brunger, A.T.

(1996) Science 271: 72-77

• PubMed: 8539602 
• DOI: https://doi.org/10.1126/science.271.5245.72
• Primary Citation Related Structures: 
  1YTT


• PubMed Abstract: 
  

  A complete and accurate set of experimental crystallographic phases to a resolution of 1.8 angstroms was obtained for a 230-residue dimeric fragment of rat mannose-binding protein A with the use of multiwavelength anomalous dispersion (MAD) phasing. An accurate image of the crystal structure could thus be obtained without resort to phases calculated from a model. Partially reduced disulfide bonds, local disorder, and differences in the mobility of chemically equivalent molecules are apparent in the experimental electron density map. A solvation layer is visible that includes well-ordered sites of hydration around polar and charged protein atoms, as well as diffuse, partially disordered solvent shells around exposed hydrophobic groups. Because the experimental phases and the resulting electron density map are free from the influence of a model, they provide a stringent test of theoretical models of macromolecular solvation, motion, and conformational heterogeneity.

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Organizational Affiliation: 
• Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.07 kDa 
• Atom Count: 1,927 
• Modeled Residue Count: 227 
• Deposited Residue Count: 230 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MANNOSE-BINDING PROTEIN A	A, B	115	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P19999 (Rattus norvegicus) Explore P19999  Go to UniProtKB:  P19999

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YB	C [auth A], D [auth A], E [auth B], F [auth B]	YTTERBIUM (III) ION Yb AWSFICBXMUKWSK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.206 (Depositor) 
• R-Value Work:  0.185 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.508	α = 90
b = 72.216	β = 90
c = 45.035	γ = 90

Software Package:

Software Name	Purpose
DENZO-SCALEPACK	data collection
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-06-10 
Deposition Author(s): Burling, F.T., Weis, W.I., Flaherty, K.M., Brunger, A.T.

Revision History  

• Version 1.0: 1996-06-10
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-11-20
  Changes: Derived calculations, Other
• Version 1.4: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary