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- PDB-4mry: Crystal Structure of Ca(2+)- discharged Y138F obelin mutant from ... -

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Basic information

Entry
Database: PDB / ID: 4mry
TitleCrystal Structure of Ca(2+)- discharged Y138F obelin mutant from Obelia longissima at 1.30 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
Biological speciesObelia longissima (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.299 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)22,7555
Polymers22,2231
Non-polymers5324
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.614, 57.112, 68.258
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-CEI / N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE / COELENTERAMIDE


Mass: 411.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H21N3O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 1.91 Å3/Da / Density % sol: 35.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium nitrate, 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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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: Sep 22, 2011
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: 1.299→50 Å / Num. all: 40375 / Num. obs: 40375 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 10.24 Å2
Reflection shellResolution: 1.3→1.32 Å / % possible all: 65.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F8P

2f8p


Resolution: 1.299→34.663 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.16 / σ(F): 1.34 / Phase error: 18.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 2000 4.96 %RANDOM
Rwork0.174 ---
all0.2211 40375 --
obs0.175 40315 94.35 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 46.25 Å2 / Biso mean: 13.5495 Å2 / Biso min: 4.51 Å2
Refinement stepCycle: LAST / Resolution: 1.299→34.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 34 297 1833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071702
X-RAY DIFFRACTIONf_angle_d1.1392318
X-RAY DIFFRACTIONf_chiral_restr0.074234
X-RAY DIFFRACTIONf_plane_restr0.006307
X-RAY DIFFRACTIONf_dihedral_angle_d17.759651
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 (%)
1.2994-1.33190.2335930.25121794188763
1.3319-1.36790.25941150.23032183229877
1.3679-1.40810.21521310.21662518264988
1.4081-1.45360.26891440.19692770291497
1.4536-1.50550.20451490.18732849299899
1.5055-1.56580.22671500.170628623012100
1.5658-1.63710.18411490.163528653014100
1.6371-1.72340.19341500.162328793029100
1.7234-1.83140.21021520.175329003052100
1.8314-1.97270.20861510.175528983049100
1.9727-2.17120.20341520.173229093061100
2.1712-2.48530.17541530.168929253078100
2.4853-3.1310.16931540.172729563110100
3.131-34.6750.17631570.16133007316497
Refinement TLS params.Method: refined / Origin x: 12.474 Å / Origin y: 23.7732 Å / Origin z: 16.7279 Å
111213212223313233
T0.0466 Å2-0.013 Å20.0098 Å2-0.0319 Å2-0.005 Å2--0.0367 Å2
L0.7163 °20.2127 °20.0257 °2-0.3533 °20.0009 °2--0.4404 °2
S0.0048 Å °0.012 Å °0.0706 Å °0.0065 Å °-0.0203 Å °-0 Å °0.0503 Å °-0.0337 Å °-0.0009 Å °
Refinement TLS groupSelection details: ALL

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