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PDBsum entry 1hn1

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protein metals Protein-protein interface(s) links
Hydrolase PDB id
1hn1
Jmol
Contents
Protein chains
1011 a.a. *
Metals
_NA ×7
_MG ×8
Waters ×401
* Residue conservation analysis
PDB id:
1hn1
Name: Hydrolase
Title: E. Coli (lac z) beta-galactosidase (orthorhombic)
Structure: Beta-galactosidase. Chain: a, b, c, d. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: lac z. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
3.00Å     R-factor:   0.148     R-free:   0.299
Authors: D.H.Juers,B.W.Matthews
Key ref:
D.H.Juers and B.W.Matthews (2001). Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions. J Mol Biol, 311, 851-862. PubMed id: 11518535 DOI: 10.1006/jmbi.2001.4891
Date:
05-Dec-00     Release date:   12-Dec-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00722  (BGAL_ECOLI) -  Beta-galactosidase
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1024 a.a.
1011 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.23  - Beta-galactosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     beta-galactosidase complex   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     9 terms  

 

 
DOI no: 10.1006/jmbi.2001.4891 J Mol Biol 311:851-862 (2001)
PubMed id: 11518535  
 
 
Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions.
D.H.Juers, B.W.Matthews.
 
  ABSTRACT  
 
Flash-freezing, which has become routine in macromolecular X-ray crystallography, causes the crystal to contract substantially. In the case of Escherichia coli beta-galactosidase the changes are reversible and are shown to be due to lattice repacking. On cooling, the area of the protein surface involved in lattice contacts increases by 50 %. There are substantial alterations in intermolecular contacts, these changes being dominated by the long, polar side-chains. For entropic reasons such side-chains, as well as surface solvent molecules, tend to be somewhat disordered at room temperature but can form extensive hydrogen-bonded networks on cooling. Low-temperature density measurements suggest that, at least in some cases, the beneficial effect of cryosolvents may be due to a density increase on vitrification which reduces the volume of bulk solvent that needs to be expelled from the crystal. Analysis of beta-galactosidase and several other proteins suggests that both intramolecular and intermolecular contact interfaces can be perturbed by cryocooling but that the changes tend to be more dramatic in the latter case. The temperature-dependence of the intermolecular interactions suggests that caution may be necessary in interpreting protein-protein and protein-nucleic acid interactions based on low-temperature crystal structures.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. (a) Bar graph showing the area contributed to lattice contacts by the different amino acid side-chains in b-galactosidase (left axis). Using the program EDPDB[43 and 44] with a probe radius of 1.4 Å, we first determined the surface area of side-chains exposed to solvent for a molecule of b-galactosidase isolated from the crystal lattice. The results are shown in gray with the scale on the right side of the Figure. The calculation was then repeated for the b-galactosidase molecule incorporated within, respectively, the room-temperature and flash-frozen crystals. The neighboring molecules in the lattice were determined with WHATIF.[45] The decrease in surface area is attributed to lattice contacts. Values for the room temperature crystals are shown in red and for the frozen crystals in blue. The scale is at the left. The error bars are ±1 standard deviation based on 19 low-temperature structures and four at room-temperature. These include various inhibitor complexes, structures of point mutants and structures determined under different solvent conditions. The low-temperature structures range in resolution from 3.0 to 1.7 Å, while those at room temperature are at about 3.0 Å resolution. (b) Temperature-dependent contributions of the different amino acids to crystal contacts in b-galactosidase. The values plotted are the differences between the blue and red histograms in (a). Each entry shows the amount by which the crystal contact area generated by a given type of amino acid changes on flash-cooling. (c). Temperature-dependent contributions of the different amino acids to crystal contacts in smaller proteins. The Figure was calculated in the same way as (b), averaging over the crystal contacts of all the structures in Table 1 (except b-galactosidase) for which the coordinates are available. The outliers (especially V and L) are mainly due to HEWL. The data set without HEWL is plotted as thin dark lines.
Figure 4.
Figure 4. An example of side-chain ordering at a lattice contact on freezing. Coordinates are from the refined models for room- temperature and low-temperature b-galactosidase (ref. [32] and PDB codes 1HN1 and 1DP0). Atoms in the room-temperature structure are colored red and the low-temperature structure cyan. Side-chains in one molecule of b-galactosidase are labeled B and in the neighboring molecule C. At room temperature the five side-chains are poorly ordered with average B-factors of about 140 Å2. On freezing the main-chain atoms move 3 Å closer together and the side-chains become ordered with average B-factors of about 30 Å2. With the participation of solvent molecules and a putative Mg2+ (in green), they generate a region of crystal contact much more extensive than that seen at room temperature. Because the low-temperature structure is to much higher resolution (1.7 Å) than that at room temperature (3.0 Å), we repeated the low-temperature refinement with the synchrotron data set truncated at 3.0 Å and also with a 3.0 Å resolution data set collected on a home source. In both cases the residues are less well defined than with 1.7 Å resolution data. However, the region is still seen to be more ordered than the room-temperature structure (average side-chain B-factors of 45 Å2 and 75 Å2 versus 140 Å2 for room temperature). This confirms that the differences seen in the room-temperature and low-temperature models are not simply due to differences in the resolution of the data.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 311, 851-862) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21525640 D.H.Juers, and M.Weik (2011).
Similarities and differences in radiation damage at 100 K versus 160 K in a crystal of thermolysin.
  J Synchrotron Radiat, 18, 329-337.  
21287621 J.E.Donald, D.W.Kulp, and W.F.Degrado (2011).
Salt bridges: Geometrically specific, designable interactions.
  Proteins, 79, 898-915.  
20944242 M.Warkentin, and R.E.Thorne (2010).
Glass transition in thaumatin crystals revealed through temperature-dependent radiation-sensitivity measurements.
  Acta Crystallogr D Biol Crystallogr, 66, 1092-1100.  
20382997 M.Weik, and J.P.Colletier (2010).
Temperature-dependent macromolecular X-ray crystallography.
  Acta Crystallogr D Biol Crystallogr, 66, 437-446.  
20382989 T.Alcorn, and D.H.Juers (2010).
Progress in rational methods of cryoprotection in macromolecular crystallography.
  Acta Crystallogr D Biol Crystallogr, 66, 366-373.  
19384990 M.R.Fleissner, D.Cascio, and W.L.Hubbell (2009).
Structural origin of weakly ordered nitroxide motion in spin-labeled proteins.
  Protein Sci, 18, 893-908.
PDB codes: 1zyt 2cuu 3g3v 3g3w 3g3x
18825126 Y.Kim, P.Quartey, H.Li, L.Volkart, C.Hatzos, C.Chang, B.Nocek, M.Cuff, J.Osipiuk, K.Tan, Y.Fan, L.Bigelow, N.Maltseva, R.Wu, M.Borovilos, E.Duggan, M.Zhou, T.A.Binkowski, R.G.Zhang, and A.Joachimiak (2008).
Large-scale evaluation of protein reductive methylation for improving protein crystallization.
  Nat Methods, 5, 853-854.  
17604315 A.Damjanović, J.L.Schlessman, C.A.Fitch, A.E.García, and B.García-Moreno E (2007).
Role of flexibility and polarity as determinants of the hydration of internal cavities and pockets in proteins.
  Biophys J, 93, 2791-2804.  
18007029 D.H.Juers, J.Lovelace, H.D.Bellamy, E.H.Snell, B.W.Matthews, and G.E.Borgstahl (2007).
Changes to crystals of Escherichia coli beta-galactosidase during room-temperature/low-temperature cycling and their relation to cryo-annealing.
  Acta Crystallogr D Biol Crystallogr, 63, 1139-1153.  
17623851 M.Andrec, D.A.Snyder, Z.Zhou, J.Young, G.T.Montelione, and R.M.Levy (2007).
A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing.
  Proteins, 69, 449-465.  
17952628 M.Warkentin, and R.E.Thorne (2007).
A general method for hyperquenching protein crystals.
  J Struct Funct Genomics, 8, 141-144.  
17473014 Z.Guo, D.Cascio, K.Hideg, T.Kálái, and W.L.Hubbell (2007).
Structural determinants of nitroxide motion in spin-labeled proteins: tertiary contact and solvent-inaccessible sites in helix G of T4 lysozyme.
  Protein Sci, 16, 1069-1086.
PDB codes: 2igc 2ntg 2nth 2ou8 2ou9
16533030 J.I.Kliegman, S.L.Griner, J.D.Helmann, R.G.Brennan, and A.Glasfeld (2006).
Structural basis for the metal-selective activation of the manganese transport regulator of Bacillus subtilis.
  Biochemistry, 45, 3493-3505.
PDB codes: 2ev0 2ev5 2ev6 2f5c 2f5d 2f5e 2f5f
20461232 M.Warkentin, V.Berejnov, N.S.Husseini, and R.E.Thorne (2006).
Hyperquenching for protein cryocrystallography.
  J Appl Crystallogr, 39, 805-811.  
16131749 B.Heras, and J.L.Martin (2005).
Post-crystallization treatments for improving diffraction quality of protein crystals.
  Acta Crystallogr D Biol Crystallogr, 61, 1173-1180.  
15869387 B.Roux (2005).
Ion conduction and selectivity in K(+) channels.
  Annu Rev Biophys Biomol Struct, 34, 153-171.  
15983410 C.U.Kim, R.Kapfer, and S.M.Gruner (2005).
High-pressure cooling of protein crystals without cryoprotectants.
  Acta Crystallogr D Biol Crystallogr, 61, 881-890.  
16041080 K.Saikrishnan, G.P.Manjunath, P.Singh, J.Jeyakanthan, Z.Dauter, K.Sekar, K.Muniyappa, and M.Vijayan (2005).
Structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologus SSBs: biological implications of structural plasticity and variability in quaternary association.
  Acta Crystallogr D Biol Crystallogr, 61, 1140-1148.
PDB codes: 1x3e 1x3f 1x3g
15608379 K.V.Dunlop, R.T.Irvin, and B.Hazes (2005).
Pros and cons of cryocrystallography: should we also collect a room-temperature data set?
  Acta Crystallogr D Biol Crystallogr, 61, 80-87.
PDB codes: 1x6p 1x6q 1x6r 1x6x 1x6y 1x6z
15051877 B.Halle (2004).
Biomolecular cryocrystallography: structural changes during flash-cooling.
  Proc Natl Acad Sci U S A, 101, 4793-4798.  
14646075 A.Vahedi-Faridi, J.Lovelace, H.D.Bellamy, E.H.Snell, and G.E.Borgstahl (2003).
Physical and structural studies on the cryocooling of insulin crystals.
  Acta Crystallogr D Biol Crystallogr, 59, 2169-2182.  
12657789 S.Kriminski, M.Kazmierczak, and R.E.Thorne (2003).
Heat transfer from protein crystals: implications for flash-cooling and X-ray beam heating.
  Acta Crystallogr D Biol Crystallogr, 59, 697-708.  
12720277 S.S.Terzyan, C.R.Bourne, P.A.Ramsland, P.C.Bourne, and A.B.Edmundson (2003).
Comparison of the three-dimensional structures of a human Bence-Jones dimer crystallized on Earth and aboard US Space Shuttle Mission STS-95.
  J Mol Recognit, 16, 83-90.
PDB codes: 1lgv 1lhz
11856832 S.Kriminski, C.L.Caylor, M.C.Nonato, K.D.Finkelstein, and R.E.Thorne (2002).
Flash-cooling and annealing of protein crystals.
  Acta Crystallogr D Biol Crystallogr, 58, 459-471.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.