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- PDB-1el4: STRUCTURE OF THE CALCIUM-REGULATED PHOTOPROTEIN OBELIN DETERMINED... -

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Basic information

Entry
Database: PDB / ID: 1el4
TitleSTRUCTURE OF THE CALCIUM-REGULATED PHOTOPROTEIN OBELIN DETERMINED BY SULFUR SAS
ComponentsOBELIN
KeywordsLUMINESCENT PROTEIN / BIOLUMINESCENCE / CALCIUM / PHOTOPROTEIN / OBELIN / SULFUR ANOMALOUS SCATTERING
Function / homology
Function and homology information


bioluminescence / calcium ion binding
Similarity search - Function
EF hand / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain ...EF hand / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
C2-HYDROXY-COELENTERAZINE / Obelin
Similarity search - Component
Biological speciesObelia longissima (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SULFUR SAS / Resolution: 1.73 Å
AuthorsLiu, Z.J. / Vysotski, E.S. / Rose, J. / Lee, J. / Wang, B.C.
Citation
Journal: Protein Sci. / Year: 2000
Title: Structure of the Ca2+-regulated photoprotein obelin at 1.7 A resolution determined directly from its sulfur substructure.
Authors: Liu, Z.J. / Vysotski, E.S. / Chen, C.J. / Rose, J.P. / Lee, J. / Wang, B.C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Preparation and preliminary study of crystals of the recombinant calcium-regulated photoprotein obelin from the bioluminescent hydroid obelia longissima
Authors: Vysotski, E.S. / Liu, Z.J. / Rose, J. / Wang, B.C. / Lee, J.
History
DepositionMar 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OBELIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7303
Polymers22,2551
Non-polymers4752
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.562, 81.562, 86.088
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
DetailsThe biological assembly is a monomer.

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Components

#1: Protein OBELIN / OBL


Mass: 22254.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Obelia longissima (invertebrata) / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q27709
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CTZ / C2-HYDROXY-COELENTERAZINE / 8-BENZYL-2-HYDROXY-2-(4-HYDROXY-BENZYL)-6-(4-HYDROXY-PHENYL)-2H-IMIDAZO[1,2-A]PYRAZIN-3-ONE


Mass: 439.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H21N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 62 %
Description: STRUCTURE DETERMINED USING THE SULFUR SAS SIGNAL RECORDED AT ID17, APS USING 1.74 ANGSTROM X-RAYS (SEE REMARK 3 REFINEMENT DETAILS)
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: HANGING DROP VAPOR DIFFUSION USING 5 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10 MG/ML) AND RESERVOIR SOLUTION: CONTAINING 1.4 M SODIUM CITRATE, PH 6.0., VAPOR ...Details: HANGING DROP VAPOR DIFFUSION USING 5 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10 MG/ML) AND RESERVOIR SOLUTION: CONTAINING 1.4 M SODIUM CITRATE, PH 6.0., VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7.4
Details: Vysotski, E.S., (1999) Acta Crystallogr., Sect.D, 55, 1965.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMpotassium/sodium phosphate1drop
21 mMEDTA1drop
310 mg/mlprotein1drop
41.4 Msodium citrate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONAPS 17-ID11.74
SYNCHROTRONAPS 19-ID20.94
SYNCHROTRONALS 5.0.231
Detector
TypeIDDetectorDate
MARRESEARCH1CCDSep 18, 1999
APS-12CCDJun 10, 1999
ADSC QUANTUM 43CCDApr 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.741
20.941
311
ReflectionResolution: 1.73→20 Å / Num. all: 33058 / Num. obs: 33694 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 37.6
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 5 % / Rmerge(I) obs: 0.216 / Num. unique all: 3274 / % possible all: 97.1
Reflection
*PLUS
Num. all: 33694 / Num. obs: 33058

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Processing

Software
NameVersionClassification
SOLVEFOLLOWED BY ISASphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
ISASphasing
RefinementMethod to determine structure: SULFUR SAS / Resolution: 1.73→19.84 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 260910.23 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: THE STRUCTURE WAS DETERMINED USING SINGLE WAVELENGTH ANOMALOUS SCATTERING DATA RECORDED FOR THE NATIVE PROTEIN. DATA WERE RECORDED ON TWO OBELIN CRYSTALS TO 2.5 ANGSTROMS RESOLUTION AT ...Details: THE STRUCTURE WAS DETERMINED USING SINGLE WAVELENGTH ANOMALOUS SCATTERING DATA RECORDED FOR THE NATIVE PROTEIN. DATA WERE RECORDED ON TWO OBELIN CRYSTALS TO 2.5 ANGSTROMS RESOLUTION AT BEAMLINE ID-17 (IMCA-CAT), ADVANCED PHOTON SOURCE (APS), ARGONNE NATIONAL LABORATORY USING A MARRESEARCH 165 MM CCD DETECTOR AND 1.74 ANGSTROM X-RAYS. A DATA COLLECTION STRATEGY (HKL2000) WAS DETERMINED FROM THE INITIAL IMAGE TO GIVE THE STARTING AND ENDING POINTS OF THE DATA COLLECTION TO INSURE A MINIMUM DATA COMPLETENESS OF 98 PERCENT. DATA WERE COLLECTED USING THE "FREIDEL FLIP" METHOD. DATA PROCESSING WAS CARRIED OUT USING HKL2000. THE PROCESSED DATA FORMING THE TWO DATA SETS WERE MERGED TO INCREASE REDUNDANCY (WU, ET AL., (2000) J. PROT. PEP. LETTS. 7, 25-32) AND SOLVE WAS USED TO DETERMINE THE SIX OF THE EIGHT SULFUR ATOM POSITIONS. PHASES WAS USED TO REFINE THE SULFUR POSITIONS AND TO LOCATE THE REMAINING SULFUR SITES BY BIJVOET DIFFERENCE FOURIER ANALYSIS. THREE ADDITIONAL SITES WERE IDENTIFIED SUGGESTING THAT ONE OF THE SULFUR SITES WAS MOST PROBABLY AN ANOMALOUS SOLVENT SUCH AS CHLORIDE. ALL ANOMALOUS SITES WERE TREATED AS SULFUR FOR THE PHASE CALCULATIONS. THE NINE SULFUR SITES WERE USED TO ESTIMATE THE INITIAL PROTEIN PHASES AT 3 ANGSTROM RESOLUTION USING SOLVENT FLATTENING (ISAS, WANG, (1985) METHODS ENZYMOL. 115, 90 112). A PRELIMINARY CHAIN TRACE WAS DONE USING THE 3.0 ANGSTROM MAP. SEQUENCE ASSIGNMENT WAS BASED ON 8 SULFUR ATOM POSITIONS. THE MODEL, 99 PERCENT COMPLETE WAS BUILT USING THE 3.0 ANGSTROM SAS MAP. RESIDUE 1 WAS NOT OBSERVED IN THE ELECTRON DENSITY AMPS AND IS PRESUMED TO BE DISORDERED. THE RESOLUTION OF THE STRUCTURE WAS THEN EXTENDED TO 1.73 ANGSTROMS RESOLUTION DURING THE FINAL STAGES OF REFINEMENT USING A MERGED DATA SET COLLECTED FROM A SINGLE CRYSTAL RECORDED AT APS (BEAMLINE ID19, WAVELENGTH 0.94 ANGSTROMS) AND AT ALS (BEAMLINE 5.0.2, WAVELENGTH 1.0 ANGSTROMS).
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2665 8.1 %RANDOM
Rwork0.188 ---
all0.191 33058 --
obs0.191 33058 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.158 Å2 / ksol: 0.370428 e/Å3
Displacement parametersBiso mean: 18.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20.98 Å20 Å2
2--0.87 Å20 Å2
3----1.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.73→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 34 266 1856
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it2.482
X-RAY DIFFRACTIONc_scangle_it3.592.5
LS refinement shellResolution: 1.73→1.84 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.302 372 7.5 %
Rwork0.261 4611 -
obs--88.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3CROM5.PARCROM5.TOP
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 8.1 % / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.302 / % reflection Rfree: 7.5 % / Rfactor Rwork: 0.261

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