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- PDB-4mrx: Crystal Structure of Y138F obelin mutant from Obelia longissima a... -

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Basic information

Entry
Database: PDB / ID: 4mrx
TitleCrystal Structure of Y138F obelin mutant from Obelia longissima at 1.72 Angstrom resolution
ComponentsObelin
KeywordsLUMINESCENT PROTEIN / calcium binding / EF-hand
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-HYDROPEROXY-COELENTERAZINE / Obelin
Similarity search - Component
Biological speciesObelia longissima (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.718 Å
AuthorsNatashin, P.V. / Ding, W. / Eremeeva, E.V. / Markova, S.V. / Lee, J. / Vysotski, E.S. / Liu, Z.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structures of the Ca2+-regulated photoprotein obelin Y138F mutant before and after bioluminescence support the catalytic function of a water molecule in the reaction.
Authors: Natashin, P.V. / Ding, W. / Eremeeva, E.V. / Markova, S.V. / Lee, J. / Vysotski, E.S. / Liu, Z.J.
History
DepositionSep 17, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Obelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6782
Polymers22,2231
Non-polymers4551
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.491, 73.491, 53.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Obelin / OBL


Mass: 22222.904 Da / Num. of mol.: 1 / Mutation: S2A, Y138F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Obelia longissima (invertebrata) / Plasmid: pOL-138F / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Gold / References: UniProt: Q27709
#2: Chemical ChemComp-CZH / C2-HYDROPEROXY-COELENTERAZINE / 8-BENZYL-2-HYDROPEROXY-2-(4-HYDROXY-BENZYL)-6-(4-HYDROXY-PHENYL)-2H-IMIDAZO[1,2-A]PYRAZIN-3-ONE


Mass: 455.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H21N3O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.1M DL-Malic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 25, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.718→50 Å / Num. all: 30654 / Num. obs: 30654 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 21.28 Å2
Reflection shellResolution: 1.72→1.78 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QV0

1qv0


Resolution: 1.718→37.357 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.12 / σ(F): 1.35 / Phase error: 15.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1692 1998 6.52 %RANDOM
Rwork0.14 ---
all0.1736 40315 --
obs0.1419 30654 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.72 Å2 / Biso mean: 26.3736 Å2 / Biso min: 11.49 Å2
Refinement stepCycle: LAST / Resolution: 1.718→37.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 34 298 1846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181688
X-RAY DIFFRACTIONf_angle_d1.7352299
X-RAY DIFFRACTIONf_chiral_restr0.123232
X-RAY DIFFRACTIONf_plane_restr0.009303
X-RAY DIFFRACTIONf_dihedral_angle_d15.034633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7183-1.76120.20761390.17411989212899
1.7612-1.80880.19091440.165620272171100
1.8088-1.86210.21091440.169520452189100
1.8621-1.92220.17941430.148220472190100
1.9222-1.99090.18771440.143320292173100
1.9909-2.07060.16931370.139120352172100
2.0706-2.16480.18011450.136320582203100
2.1648-2.27890.16021410.131620422183100
2.2789-2.42170.15961410.131220172158100
2.4217-2.60860.17451460.155320512197100
2.6086-2.8710.16091440.161420552199100
2.871-3.28630.21431410.154920552196100
3.2863-4.13950.16431420.124920782220100
4.1395-37.36570.13481470.122221042251100
Refinement TLS params.Method: refined / Origin x: 69.6173 Å / Origin y: 24.76 Å / Origin z: 22.9557 Å
111213212223313233
T0.1388 Å2-0.0196 Å20.0213 Å2-0.0844 Å20.0037 Å2--0.1093 Å2
L1.0475 °2-0.1271 °2-0.0924 °2-2.3126 °2-0.1686 °2--1.3847 °2
S-0.034 Å °0.043 Å °-0.0131 Å °-0.0618 Å °0.1166 Å °0.1646 Å °-0.0892 Å °-0.0352 Å °0.0067 Å °
Refinement TLS groupSelection details: ALL

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