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- PDB-4n1g: Crystal Structure of Ca(2+)- discharged F88Y obelin mutant from O... -

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Basic information

Entry
Database: PDB / ID: 4n1g
TitleCrystal Structure of Ca(2+)- discharged F88Y obelin mutant from Obelia longissima at 1.50 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: 1.5 Å
AuthorsNatashin, P.V. / Markova, S.V. / Lee, J. / Vysotski, E.S. / Liu, Z.J.
CitationJournal: Febs J. / Year: 2014
Title: Crystal structures of the F88Y obelin mutant before and after bioluminescence provide molecular insight into spectral tuning among hydromedusan photoproteins
Authors: Natashin, P.V. / Markova, S.V. / Lee, J. / Vysotski, E.S. / Liu, Z.J.
History
DepositionOct 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
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_ncs_dom_lim / struct_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_asym_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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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
B: Obelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,57310
Polymers44,5102
Non-polymers1,0638
Water10,196566
1
A: Obelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7875
Polymers22,2551
Non-polymers5324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Obelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7875
Polymers22,2551
Non-polymers5324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.920, 85.127, 90.088
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 2 - 195 / Label seq-ID: 2 - 195

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Obelin / OBL


Mass: 22254.904 Da / Num. of mol.: 2 / Mutation: S2A, F88Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Obelia longissima (invertebrata) / Plasmid: pET19 / 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.: 2 / Source method: obtained synthetically / Formula: C25H21N3O3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.2M ammonium sulfate, 2% PEG 400, 0.1M HEPES-Na, pH 7.5, 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: Apr 8, 2013
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: 1.5→50 Å / Num. all: 58909 / Num. obs: 58909 / % possible obs: 77.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 17.12 Å2
Reflection shellResolution: 1.5→1.55 Å / % possible all: 8.61

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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: 2F8P

2f8p


Resolution: 1.5→49.541 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.15 / σ(F): 1.34 / Phase error: 24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 2001 3.4 %RANDOM
Rwork0.1688 ---
all0.3375 58909 --
obs0.1701 58830 77.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75 Å2 / Biso mean: 22.6475 Å2 / Biso min: 6.67 Å2
Refinement stepCycle: LAST / Resolution: 1.5→49.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3114 0 68 566 3748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023341
X-RAY DIFFRACTIONf_angle_d1.7284528
X-RAY DIFFRACTIONf_chiral_restr0.082453
X-RAY DIFFRACTIONf_plane_restr0.01593
X-RAY DIFFRACTIONf_dihedral_angle_d16.8811238
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1739X-RAY DIFFRACTION7.183TORSIONAL
12B1739X-RAY DIFFRACTION7.183TORSIONAL
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 (%)
1.4999-1.53740.4413100.33953523627
1.5374-1.5790.3911320.331484287416
1.579-1.62550.3859580.28491674173232
1.6255-1.67790.2899990.25472865296455
1.6779-1.73790.27491520.234111426379
1.7379-1.80750.28591760.21274882505895
1.8075-1.88980.20961830.193551745357100
1.8898-1.98940.21971820.179351765358100
1.9894-2.1140.20541750.180652085383100
2.114-2.27730.20671840.165652245408100
2.2773-2.50640.22311830.165252525435100
2.5064-2.86910.23111830.179752515434100
2.8691-3.61460.19151900.149753225512100
3.6146-49.5680.16621940.142854965690100
Refinement TLS params.Method: refined / Origin x: 29.5649 Å / Origin y: 34.2587 Å / Origin z: 35.204 Å
111213212223313233
T0.0842 Å2-0.0149 Å2-0.0085 Å2-0.0742 Å20.019 Å2--0.0865 Å2
L0.5204 °2-0.1993 °2-0.301 °2-0.4293 °20.2333 °2--0.5942 °2
S0.0448 Å °0.0221 Å °0.0433 Å °-0.0207 Å °-0.0093 Å °-0.0277 Å °-0.0257 Å °-0.0143 Å °-0.0417 Å °
Refinement TLS groupSelection details: ALL

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