Experimental Data Snapshot

  • Resolution: 1.15 Å
  • R-Value Free: 0.162 
  • R-Value Observed: 0.122 

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Crystallographic evaluation of internal motion of human alpha-lactalbumin refined by full-matrix least-squares method.

Harata, K.Abe, Y.Muraki, M.

(1999) J Mol Biol 287: 347-358

  • DOI: https://doi.org/10.1006/jmbi.1999.2598
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The low temperature form of human alpha-lactalbumin (HAL) was crystallized from a 2H2O solution and its structure was refined to the R value of 0.119 at 1.15 A resolution by the full-matrix least-squares method. Average estimated standard deviations of atomic parameters for non-hydrogen atoms were 0.038 A for coordinates and 0.044 A2 for anisotropic temperature factors (Uij). The magnitude of equivalent isotropic temperature factors (Ueqv) was highly correlated with the distance from the molecular centroid and fitted to a quadratic equation as a function of atomic coordinates. The atomic thermal motion was rather isotropic in the core region and the anisotropy increased towards the molecular surface. The statistical analysis revealed the out-of-plane motion of main-chain oxygen atoms, indicating that peptide groups are in rotational vibration around a Calpha.Calpha axis. The TLS model, which describes the rigid-body motion in terms of translation, libration, and screw motions, was adopted for the evaluation of the molecular motion and the TLS parameters were determined by the least-squares fit to Uij. The reproduced Ueqvcal from the TLS parameters was in fair agreement with observed Ueqv, but differences were found in regions of residues, 5-22, 44-48, 70-75, and 121-123, where Ueqv was larger than Ueqvcal because of large local motions. To evaluate the internal motion of HAL, the contribution of the rigid-body motion was determined to be 42.4 % of Ueqv in magnitude, which was the highest estimation to satisfy the condition that the Uijint tensors of the internal motion have positive eigen values. The internal motion represented with atomic thermal ellipsoids clearly showed local motions different from those observed in chicken-type lysozymes which have a backbone structure very similar to HAL. The result indicates that the internal motion is closely related to biological function of proteins.

  • Organizational Affiliation

    Biomolecules Department, National Institute of Bioscience and Human-Technology, 1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan. harata@nibh.go.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (ALPHA-LACTALBUMIN)123Homo sapiensMutation(s): 0 
Gene Names: LALBALYZL7
UniProt & NIH Common Fund Data Resources
Find proteins for P00709 (Homo sapiens)
Explore P00709 
Go to UniProtKB:  P00709
PHAROS:  P00709
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00709
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.15 Å
  • R-Value Free: 0.162 
  • R-Value Observed: 0.122 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.19α = 90
b = 49.55β = 90
c = 64.2γ = 90
Software Package:
Software NamePurpose
MADNESSdata collection
MERGEFdata reduction
X-PLORmodel building
MADNESSdata reduction
MERGEFdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-03-31
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description