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PDBsum entry 1el4
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Luminescent protein PDB id
1el4

 

 

 

 

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JSmol PyMol  
Contents
Protein chain
194 a.a. *
Ligands
CTZ
Metals
_CL
Waters ×266
* Residue conservation analysis
PDB id:
1el4
Name: Luminescent protein
Title: Structure of the calcium-regulated photoprotein obelin determined by sulfur sas
Structure: Obelin. Chain: a. Synonym: obl. Engineered: yes
Source: Obelia longissima. Organism_taxid: 32570. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.73Å     R-factor:   0.188     R-free:   0.205
Authors: Z.J.Liu,E.S.Vysotski,J.Rose,J.Lee,B.C.Wang
Key ref: Z.J.Liu et al. (2000). Structure of the Ca2+-regulated photoprotein obelin at 1.7 A resolution determined directly from its sulfur substructure. Protein Sci, 9, 2085-2093. PubMed id: 11152120 DOI: 10.1110/ps.9.11.2085
Date:
13-Mar-00     Release date:   13-Mar-01    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q27709  (OBL_OBELO) -  Obelin from Obelia longissima
Seq:
Struc: 		195 a.a.
194 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1110/ps.9.11.2085 Protein Sci 9:2085-2093 (2000)
PubMed id: 11152120  
 
 
Structure of the Ca2+-regulated photoprotein obelin at 1.7 A resolution determined directly from its sulfur substructure.
Z.J.Liu, E.S.Vysotski, C.J.Chen, J.P.Rose, J.Lee, B.C.Wang.
 
  ABSTRACT  
 
The crystal structure of the photoprotein obelin (22.2 kDa) from Obelia longissima has been determined and refined to 1.7 A resolution. Contrary to the prediction of a peroxide, the noncovalently bound substrate, coelenterazine, has only a single oxygen atom bound at the C2-position. The protein-coelenterazine 2-oxy complex observed in the crystals is photo-active because, in the presence of calcium ion, bioluminescence emission within the crystal is observed. This structure represents only the second de novo protein structure determined using the anomalous scattering signal of the sulfur substructure in the crystal. The method used here is theoretically different from that used for crambin in 1981 (4.72 kDa) and represents a significant advancement in protein crystal structure determination.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21336798 T.N.Kirillova, M.A.Gerasimova, E.V.Nemtseva, and N.S.Kudryasheva (2011).
Effect of halogenated fluorescent compounds on bioluminescent reactions.
  Anal Bioanal Chem, 400, 343-351.  
22011470 Z.J.Liu, L.Chen, D.Wu, W.Ding, H.Zhang, W.Zhou, Z.Q.Fu, and B.C.Wang (2011).
A multi-dataset data-collection strategy produces better diffraction data.
  Acta Crystallogr A, 67, 544-549.  
  21141672 S.H.Haddock, M.A.Moline, and J.F.Case (2010).
Bioluminescence in the sea.
  Ann Rev Mar Sci, 2, 443-493.  
20442953 S.V.Markova, L.P.Burakova, L.A.Frank, S.Golz, K.A.Korostileva, and E.S.Vysotski (2010).
Green-fluorescent protein from the bioluminescent jellyfish Clytia gregaria: cDNA cloning, expression, and characterization of novel recombinant protein.
  Photochem Photobiol Sci, 9, 757-765.  
19324092 J.Abendroth, D.D.Mitchell, K.V.Korotkov, T.L.Johnson, A.Kreger, M.Sandkvist, and W.G.Hol (2009).
The three-dimensional structure of the cytoplasmic domains of EpsF from the type 2 secretion system of Vibrio cholerae.
  J Struct Biol, 166, 303-315.
PDB codes: 2vma 2vmb 3c1q
19237744 K.Lakomek, A.Dickmanns, U.Mueller, K.Kollmann, F.Deuschl, A.Berndt, T.Lübke, and R.Ficner (2009).
De novo sulfur SAD phasing of the lysosomal 66.3 kDa protein from mouse.
  Acta Crystallogr D Biol Crystallogr, 65, 220-228.
PDB code: 3fbx
18595733 G.A.Stepanyuk, H.Xu, C.K.Wu, S.V.Markova, J.Lee, E.S.Vysotski, and B.C.Wang (2008).
Expression, purification and characterization of the secreted luciferase of the copepod Metridia longa from Sf9 insect cells.
  Protein Expr Purif, 61, 142-148.  
18385886 G.A.Stepanyuk, Z.J.Liu, S.S.Markova, L.A.Frank, J.Lee, E.S.Vysotski, and B.C.Wang (2008).
Crystal structure of coelenterazine-binding protein from Renilla muelleri at 1.7 A: why it is not a calcium-regulated photoprotein.
  Photochem Photobiol Sci, 7, 442-447.
PDB codes: 2hps 2hq8
18359861 J.Woo, M.H.Howell, and A.G.von Arnim (2008).
Structure-function studies on the active site of the coelenterazine-dependent luciferase from Renilla.
  Protein Sci, 17, 725-735.  
18604525 L.A.Frank, V.V.Borisova, S.V.Markova, N.P.Malikova, G.A.Stepanyuk, and E.S.Vysotski (2008).
Violet and greenish photoprotein obelin mutants for reporter applications in dual-color assay.
  Anal Bioanal Chem, 391, 2891-2896.  
18264586 M.S.Titushin, S.V.Markova, L.A.Frank, N.P.Malikova, G.A.Stepanyuk, J.Lee, and E.S.Vysotski (2008).
Coelenterazine-binding protein of Renilla muelleri: cDNA cloning, overexpression, and characterization as a substrate of luciferase.
  Photochem Photobiol Sci, 7, 189-196.  
19088753 V.V.Borisova, I.A.Pyshnaya, D.V.Pyshnyi, and L.A.Frank (2008).
[A highly sensitive and rapid method for the detection of DNA fragments using the photoprotein obelin as a reporter.]
  Bioorg Khim, 34, 792-798.  
17237922 T.N.Kirillova, and N.S.Kudryasheva (2007).
Effect of heavy atoms in bioluminescent reactions.
  Anal Bioanal Chem, 387, 2009-2016.  
17057349 A.Wagner, M.Pieren, C.Schulze-Briese, K.Ballmer-Hofer, and A.E.Prota (2006).
Structure determination of VEGF-E by sulfur SAD.
  Acta Crystallogr D Biol Crystallogr, 62, 1430-1434.  
16790924 C.U.Kim, Q.Hao, and S.M.Gruner (2006).
Solution of protein crystallographic structures by high-pressure cryocooling and noble-gas phasing.
  Acta Crystallogr D Biol Crystallogr, 62, 687-694.  
16790926 G.N.Sarma, and P.A.Karplus (2006).
In-house sulfur SAD phasing: a case study of the effects of data quality and resolution cutoffs.
  Acta Crystallogr D Biol Crystallogr, 62, 707-716.  
16510975 H.Miyatake, T.Hasegawa, and A.Yamano (2006).
New methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL).
  Acta Crystallogr D Biol Crystallogr, 62, 280-289.
PDB codes: 2d8o 2d8p 2d8w 2d91 2d97 2d98
16769886 L.Tricoire, K.Tsuzuki, O.Courjean, N.Gibelin, G.Bourout, J.Rossier, and B.Lambolez (2006).
Calcium dependence of aequorin bioluminescence dissected by random mutagenesis.
  Proc Natl Acad Sci U S A, 103, 9500-9505.  
16467137 Z.J.Liu, G.A.Stepanyuk, E.S.Vysotski, J.Lee, S.V.Markova, N.P.Malikova, and B.C.Wang (2006).
Crystal structure of obelin after Ca2+-triggered bioluminescence suggests neutral coelenteramide as the primary excited state.
  Proc Natl Acad Sci U S A, 103, 2570-2575.
PDB code: 2f8p
16131760 C.Mueller-Dieckmann, S.Panjikar, P.A.Tucker, and M.S.Weiss (2005).
On the routine use of soft X-rays in macromolecular crystallography. Part III. The optimal data-collection wavelength.
  Acta Crystallogr D Biol Crystallogr, 61, 1263-1272.
PDB codes: 2a7a 2a7b 2a7c 2a7d 2a7e 2a7f 2a7g 2a7h 2a7i 2a7j
16041070 D.Roeser, A.Dickmanns, K.Gasow, and M.G.Rudolph (2005).
De novo calcium/sulfur SAD phasing of the human formylglycine-generating enzyme using in-house data.
  Acta Crystallogr D Biol Crystallogr, 61, 1057-1066.
PDB code: 1z70
15983419 H.Xu, C.Yang, L.Chen, I.A.Kataeva, W.Tempel, D.Lee, J.E.Habel, D.Nguyen, J.W.Pflugrath, J.D.Ferrara, W.B.Arendall, J.S.Richardson, D.C.Richardson, Z.J.Liu, M.G.Newton, J.P.Rose, and B.C.Wang (2005).
Away from the edge II: in-house Se-SAS phasing with chromium radiation.
  Acta Crystallogr D Biol Crystallogr, 61, 960-966.
PDB code: 1xho
15968116 K.Djinović Carugo, J.R.Helliwell, H.Stuhrmann, and M.S.Weiss (2005).
Softer and soft X-rays in macromolecular crystallography.
  J Synchrotron Radiat, 12, 410-419.  
15689515 L.Deng, E.S.Vysotski, S.V.Markova, Z.J.Liu, J.Lee, J.Rose, and B.C.Wang (2005).
All three Ca2+-binding loops of photoproteins bind calcium ions: the crystal structures of calcium-loaded apo-aequorin and apo-obelin.
  Protein Sci, 14, 663-675.
PDB codes: 1sl7 1sl8
15665092 L.W.Schultz, L.Liu, M.Cegielski, and J.W.Hastings (2005).
Crystal structure of a pH-regulated luciferase catalyzing the bioluminescent oxidation of an open tetrapyrrole.
  Proc Natl Acad Sci U S A, 102, 1378-1383.
PDB code: 1vpr
16239732 N.Watanabe, Y.Kitago, I.Tanaka, J.Wang, Y.Gu, C.Zheng, and H.Fan (2005).
Comparison of phasing methods for sulfur-SAD using in-house chromium radiation: case studies for standard proteins and a 69 kDa protein.
  Acta Crystallogr D Biol Crystallogr, 61, 1533-1540.  
15608382 P.S.Salgado, M.A.Walsh, M.R.Laurila, D.I.Stuart, and J.M.Grimes (2005).
Going soft and SAD with manganese.
  Acta Crystallogr D Biol Crystallogr, 61, 108-111.  
16041066 R.A.Nagem, A.L.Ambrosio, A.L.Rojas, M.V.Navarro, A.M.Golubev, R.C.Garratt, and I.Polikarpov (2005).
Getting the most out of X-ray home sources.
  Acta Crystallogr D Biol Crystallogr, 61, 1022-1030.  
15632284 S.Toma, K.T.Chong, A.Nakagawa, K.Teranishi, S.Inouye, and O.Shimomura (2005).
The crystal structures of semi-synthetic aequorins.
  Protein Sci, 14, 409-416.
PDB codes: 1uhh 1uhi 1uhj 1uhk
16131763 U.A.Ramagopal, Z.Dauter, R.Thirumuruhan, E.Fedorov, and S.C.Almo (2005).
Radiation-induced site-specific damage of mercury derivatives: phasing and implications.
  Acta Crystallogr D Biol Crystallogr, 61, 1289-1298.  
16041065 Y.Kitago, N.Watanabe, and I.Tanaka (2005).
Structure determination of a novel protein by sulfur SAD using chromium radiation in combination with a new crystal-mounting method.
  Acta Crystallogr D Biol Crystallogr, 61, 1013-1021.
PDB codes: 2czz 2e6u
15930619 Z.J.Liu, W.Tempel, J.D.Ng, D.Lin, A.K.Shah, L.Chen, P.S.Horanyi, J.E.Habel, I.A.Kataeva, H.Xu, H.Yang, J.C.Chang, L.Huang, S.H.Chang, W.Zhou, D.Lee, J.L.Praissman, H.Zhang, M.G.Newton, J.P.Rose, J.S.Richardson, D.C.Richardson, and B.C.Wang (2005).
The high-throughput protein-to-structure pipeline at SECSG.
  Acta Crystallogr D Biol Crystallogr, 61, 679-684.  
15583401 C.E.Stevenson, A.Tanner, L.Bowater, S.Bornemann, and D.M.Lawson (2004).
SAD at home: solving the structure of oxalate decarboxylase with the anomalous signal from manganese using X-ray data collected on a home source.
  Acta Crystallogr D Biol Crystallogr, 60, 2403-2406.  
14684889 C.Mueller-Dieckmann, M.Polentarutti, K.Djinovic Carugo, S.Panjikar, P.A.Tucker, and M.S.Weiss (2004).
On the routine use of soft X-rays in macromolecular crystallography. Part II. Data-collection wavelength and scaling models.
  Acta Crystallogr D Biol Crystallogr, 60, 28-38.
PDB code: 1uo6
14747700 J.G.Olsen, C.Flensburg, O.Olsen, G.Bricogne, and A.Henriksen (2004).
Solving the structure of the bubble protein using the anomalous sulfur signal from single-crystal in-house Cu Kalpha diffraction data only.
  Acta Crystallogr D Biol Crystallogr, 60, 250-255.
PDB code: 1uoy
15213386 J.W.Wang, J.R.Chen, Y.X.Gu, C.D.Zheng, F.Jiang, H.F.Fan, T.C.Terwilliger, and Q.Hao (2004).
SAD phasing by combination of direct methods with the SOLVE/RESOLVE procedure.
  Acta Crystallogr D Biol Crystallogr, 60, 1244-1253.  
14993663 K.I.Varughese, Z.M.Ruggeri, and R.Celikel (2004).
Platinum-induced space-group transformation in crystals of the platelet glycoprotein Ib alpha N-terminal domain.
  Acta Crystallogr D Biol Crystallogr, 60, 405-411.
PDB code: 1qyy
15333929 K.Sekar, V.Rajakannan, D.Velmurugan, T.Yamane, R.Thirumurugan, M.Dauter, and Z.Dauter (2004).
A redetermination of the structure of the triple mutant (K53,56,120M) of phospholipase A2 at 1.6 A resolution using sulfur-SAS at 1.54 A wavelength.
  Acta Crystallogr D Biol Crystallogr, 60, 1586-1590.
PDB code: 1vkq
14993677 L.Deng, S.V.Markova, E.S.Vysotski, Z.J.Liu, J.Lee, J.Rose, and B.C.Wang (2004).
Preparation and X-ray crystallographic analysis of the Ca2+-discharged photoprotein obelin.
  Acta Crystallogr D Biol Crystallogr, 60, 512-514.  
15039557 M.S.Weiss, G.Mander, R.Hedderich, K.Diederichs, U.Ermler, and E.Warkentin (2004).
Determination of a novel structure by a combination of long-wavelength sulfur phasing and radiation-damage-induced phasing.
  Acta Crystallogr D Biol Crystallogr, 60, 686-695.
PDB code: 1sau
14993675 Z.Q.Fu, J.P.Rose, and B.C.Wang (2004).
Monitoring the anomalous scattering signal and noise levels in X-ray diffraction of crystals.
  Acta Crystallogr D Biol Crystallogr, 60, 499-506.  
14573949 C.Yang, J.W.Pflugrath, D.A.Courville, C.N.Stence, and J.D.Ferrara (2003).
Away from the edge: SAD phasing from the sulfur anomalous signal measured in-house with chromium radiation.
  Acta Crystallogr D Biol Crystallogr, 59, 1943-1957.  
14646070 J.E.Debreczeni, B.Girmann, A.Zeeck, R.Krätzner, and G.M.Sheldrick (2003).
Structure of viscotoxin A3: disulfide location from weak SAD data.
  Acta Crystallogr D Biol Crystallogr, 59, 2125-2132.
PDB code: 1okh
12554963 J.E.Debreczeni, G.Bunkóczi, B.Girmann, and G.M.Sheldrick (2003).
In-house phase determination of the lima bean trypsin inhibitor: a low-resolution sulfur-SAD case.
  Acta Crystallogr D Biol Crystallogr, 59, 393-395.
PDB code: 1h34
12777765 U.A.Ramagopal, M.Dauter, and Z.Dauter (2003).
Phasing on anomalous signal of sulfurs: what is the limit?
  Acta Crystallogr D Biol Crystallogr, 59, 1020-1027.  
12777803 U.A.Ramagopal, M.Dauter, and Z.Dauter (2003).
SAD manganese in two crystal forms of glucose isomerase.
  Acta Crystallogr D Biol Crystallogr, 59, 868-875.
PDB code: 1oad
12454470 C.T.Lemke, G.D.Smith, and P.L.Howell (2002).
S-SAD, Se-SAD and S/Se-SIRAS using Cu Kalpha radiation: why wait for synchrotron time?
  Acta Crystallogr D Biol Crystallogr, 58, 2096-2101.  
11752776 E.Micossi, W.N.Hunter, and G.A.Leonard (2002).
De novo phasing of two crystal forms of tryparedoxin II using the anomalous scattering from S atoms: a combination of small signal and medium resolution reveals this to be a general tool for solving protein crystal structures.
  Acta Crystallogr D Biol Crystallogr, 58, 21-28.
PDB codes: 1o6j 1o81
12077434 J.A.Gavira, D.Toh, J.Lopéz-Jaramillo, J.M.García-Ruíz, and J.D.Ng (2002).
Ab initio crystallographic structure determination of insulin from protein to electron density without crystal handling.
  Acta Crystallogr D Biol Crystallogr, 58, 1147-1154.  
12445769 J.Choe, S.Suresh, G.Wisedchaisri, K.J.Kennedy, M.H.Gelb, and W.G.Hol (2002).
Anomalous differences of light elements in determining precise binding modes of ligands to glycerol-3-phosphate dehydrogenase.
  Chem Biol, 9, 1189-1197.
PDB codes: 1jdj 1m66 1m67 1n1g
  12446351 J.D.Ng (2002).
Space-grown protein crystals are more useful for structure determination.
  Ann N Y Acad Sci, 974, 598-609.  
11841214 S.V.Markova, E.S.Vysotski, J.R.Blinks, L.P.Burakova, B.C.Wang, and J.Lee (2002).
Obelin from the bioluminescent marine hydroid Obelia geniculata: cloning, expression, and comparison of some properties with those of other Ca2+-regulated photoproteins.
  Biochemistry, 41, 2227-2236.  
11856836 Z.Dauter, M.Dauter, and E.Dodson (2002).
Jolly SAD.
  Acta Crystallogr D Biol Crystallogr, 58, 494-506.  
11320328 C.S.Bond, M.P.Shaw, M.S.Alphey, and W.N.Hunter (2001).
Structure of the macrocycle thiostrepton solved using the anomalous dispersion contribution of sulfur.
  Acta Crystallogr D Biol Crystallogr, 57, 755-758.
PDB code: 1e9w
11567163 C.Yang, and J.W.Pflugrath (2001).
Applications of anomalous scattering from S atoms for improved phasing of protein diffraction data collected at Cu Kalpha wavelength.
  Acta Crystallogr D Biol Crystallogr, 57, 1480-1490.  
11526314 E.J.Gordon, G.A.Leonard, S.McSweeney, and P.F.Zagalsky (2001).
The C1 subunit of alpha-crustacyanin: the de novo phasing of the crystal structure of a 40 kDa homodimeric protein using the anomalous scattering from S atoms combined with direct methods.
  Acta Crystallogr D Biol Crystallogr, 57, 1230-1237.
PDB code: 1i4u
11717517 E.S.Vysotski, Z.J.Liu, J.Rose, B.C.Wang, and J.Lee (2001).
Preparation and X-ray crystallographic analysis of recombinant obelin crystals diffracting to beyond 1.1 A.
  Acta Crystallogr D Biol Crystallogr, 57, 1919-1921.  
11566127 M.S.Weiss, T.Sicker, and R.Hilgenfeld (2001).
Soft X-rays, high redundancy, and proper scaling: a new procedure for automated protein structure determination via SAS.
  Structure, 9, 771-777.  
11572972 S.H.Haddock, T.J.Rivers, and B.H.Robison (2001).
Can coelenterates make coelenterazine? Dietary requirement for luciferin in cnidarian bioluminescence.
  Proc Natl Acad Sci U S A, 98, 11148-11151.  
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.

 

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