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- PDB-5d9c: Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined... -

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Basic information

Entry
Database: PDB / ID: 5d9c
TitleLuciferin-regenerating enzyme solved by SIRAS using XFEL (refined against Hg derivative data)
ComponentsLuciferin regenerating enzyme
KeywordsHYDROLASE / beta-prooeller
Function / homology
Function and homology information


gluconolactonase activity / L-ascorbic acid biosynthetic process / calcium ion binding
Similarity search - Function
Senescence marker protein-30 (SMP-30) / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
: / Luciferin regenerating enzyme
Similarity search - Component
Biological speciesPhotinus pyralis (common eastern firefly)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / SIRAS / Resolution: 1.6 Å
AuthorsYamashita, K. / Pan, D. / Okuda, T. / Murai, T. / Kodan, A. / Yamaguchi, T. / Gomi, K. / Kajiyama, N. / Kato, H. / Ago, H. ...Yamashita, K. / Pan, D. / Okuda, T. / Murai, T. / Kodan, A. / Yamaguchi, T. / Gomi, K. / Kajiyama, N. / Kato, H. / Ago, H. / Yamamoto, M. / Nakatsu, T.
CitationJournal: Sci Rep / Year: 2015
Title: An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Authors: Yamashita, K. / Pan, D. / Okuda, T. / Sugahara, M. / Kodan, A. / Yamaguchi, T. / Murai, T. / Gomi, K. / Kajiyama, N. / Mizohata, E. / Suzuki, M. / Nango, E. / Tono, K. / Joti, Y. / ...Authors: Yamashita, K. / Pan, D. / Okuda, T. / Sugahara, M. / Kodan, A. / Yamaguchi, T. / Murai, T. / Gomi, K. / Kajiyama, N. / Mizohata, E. / Suzuki, M. / Nango, E. / Tono, K. / Joti, Y. / Kameshima, T. / Park, J. / Song, C. / Hatsui, T. / Yabashi, M. / Iwata, S. / Kato, H. / Ago, H. / Yamamoto, M. / Nakatsu, T.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Luciferin regenerating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7455
Polymers34,2021
Non-polymers5444
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-78 kcal/mol
Surface area12690 Å2
Unit cell
Length a, b, c (Å)48.100, 77.500, 84.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Luciferin regenerating enzyme


Mass: 34201.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photinus pyralis (common eastern firefly)
Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q95YI4
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe depositors believe that residues ILE 133, TYR 268, PHE 281 are correct and that UniProt is ...The depositors believe that residues ILE 133, TYR 268, PHE 281 are correct and that UniProt is incorrect at these positions

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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: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: mixing purified LRE solution (27 mg/mL LRE, 10 mM HEPES pH 7.5, 0.1 M NaCl, 10% glycerol) and precipitant solution (35% PEG3350, 10% MPD, 0.1 M HEPES pH 7.5, 0.2 M MgCl2) at ratios between 1:2 and 1:1.6

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 0.984 Å
DetectorType: MPCCD / Detector: CCD / Date: May 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. obs: 80855 / % possible obs: 100 % / Redundancy: 106.2 % / Net I/σ(I): 1.82

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
PDB_EXTRACT3.15data extraction
SHELXDEphasing
CrystFELdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 1.6→24.712 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 2946 3.98 %
Rwork0.2021 71098 -
obs0.2034 74044 91.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.98 Å2 / Biso mean: 28.3727 Å2 / Biso min: 15.15 Å2
Refinement stepCycle: final / Resolution: 1.6→24.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 11 164 2560
Biso mean--30.13 35.6 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142470
X-RAY DIFFRACTIONf_angle_d1.4523365
X-RAY DIFFRACTIONf_chiral_restr0.068379
X-RAY DIFFRACTIONf_plane_restr0.008432
X-RAY DIFFRACTIONf_dihedral_angle_d14.011900
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.62620.4322160.459740942511
1.6262-1.65430.4146620.39921475153740
1.6543-1.68430.3611210.37672879300077
1.6843-1.71670.37651480.36193558370697
1.7167-1.75180.36181510.348536893840100
1.7518-1.78990.34341600.320836753835100
1.7899-1.83150.34691420.303837063848100
1.8315-1.87730.32561570.298136863843100
1.8773-1.9280.31351530.252737003853100
1.928-1.98470.26531560.231737003856100
1.9847-2.04870.2311560.216936563812100
2.0487-2.12190.24961480.199137403888100
2.1219-2.20680.24811540.195636963850100
2.2068-2.30720.20371500.186936793829100
2.3072-2.42870.21781550.192336933848100
2.4287-2.58080.23291540.187736923846100
2.5808-2.77980.25911560.18336853841100
2.7798-3.05910.19651500.189736943844100
3.0591-3.50060.23671520.172737033855100
3.5006-4.40640.21611530.164737083861100
4.4064-24.7150.17641520.18136753827100

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