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- PDB-5gx5: Luciferin-regenerating enzyme collected with serial synchrotron r... -

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Basic information

Entry
Database: PDB / ID: 5gx5
TitleLuciferin-regenerating enzyme collected with serial synchrotron rotational crystallography with accumulated dose of 26 MGy (23rd measurement)
ComponentsLuciferin regenerating enzyme
KeywordsHYDROLASE / BETA-PROOELLER
Function / homology
Function and homology information


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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsHasegawa, K. / Yamashita, K. / Murai, T. / Nuemket, N. / Hirata, K. / Ueno, G. / Ago, H. / Nakatsu, T. / Kumasaka, T. / Yamamoto, M.
CitationJournal: J Synchrotron Radiat / Year: 2017
Title: Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography
Authors: Hasegawa, K. / Yamashita, K. / Murai, T. / Nuemket, N. / Hirata, K. / Ueno, G. / Ago, H. / Nakatsu, T. / Kumasaka, T. / Yamamoto, M.
History
DepositionSep 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Luciferin regenerating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7556
Polymers34,2021
Non-polymers5535
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-28 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.594, 77.119, 84.604
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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: pET15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q95YI4

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Non-polymers , 5 types, 217 molecules

#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsDepositors state that the protein sequence should be the same as the database sequence UNP Q95YI4. ...Depositors state that the protein sequence should be the same as the database sequence UNP Q95YI4. The accession number is AB062786.2 for the sequence.

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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: 2.27 Å3/Da / Density % sol: 45.81 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: 150 uL of purified LRE solution (30 mg/ml LRE, 10 mM HEPES(pH7.5), 100 mM NaCl, 10 %(v/v) glycerol) was mixed with 240 uL of precipitant solution (31.3 %(w/v) PEG3350, 0.1 M HEPES(pH7.5), 10 ...Details: 150 uL of purified LRE solution (30 mg/ml LRE, 10 mM HEPES(pH7.5), 100 mM NaCl, 10 %(v/v) glycerol) was mixed with 240 uL of precipitant solution (31.3 %(w/v) PEG3350, 0.1 M HEPES(pH7.5), 10 %(v/v) MPD, 0.2 M MgCl2) and 15 uL of seed-crystal solution (31.3 %(w/v) PEG3350, 0.1 M HEPES(pH7.5), 10 %(v/v) MPD, 0.2 M MgCl2, 0.1 M NaCl, 5 %(v/v) glycerol)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9839 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 30, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9839 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 79457 / % possible obs: 100 % / Redundancy: 27.894 % / CC1/2: 0.9904369 / Net I/σ(I): 4.144122 / Num. measured all: 2216376
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsCC1/2Diffraction-ID% possible all
3.328-5029.312.850.98931100
2.641-3.32827.28.050.97791100
2.307-2.64128.85.610.95191100
2.096-2.30729.54.150.90751100
1.946-2.09625.92.690.80961100
1.832-1.94628.11.750.58991100
1.74-1.83228.51.050.32821100
1.664-1.7428.60.680.15471100
1.6-1.66425.10.440.07391100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSOct 15, 2015data processing
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5GTQ

5gtq


Resolution: 1.6→42.302 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.53 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2341 3118 3.96 %
Rwork0.2098 75601 -
obs0.2108 78719 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.02 Å2 / Biso mean: 25.1018 Å2 / Biso min: 13.15 Å2
Refinement stepCycle: final / Resolution: 1.6→42.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 24 212 2621
Biso mean--31.66 36.95 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072461
X-RAY DIFFRACTIONf_angle_d0.8533346
X-RAY DIFFRACTIONf_chiral_restr0.059375
X-RAY DIFFRACTIONf_plane_restr0.005427
X-RAY DIFFRACTIONf_dihedral_angle_d13.6741452
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.6250.44491300.39143166329692
1.625-1.65170.40331320.38783275340794
1.6517-1.68010.39341390.36243355349497
1.6801-1.71070.3571400.35763464360499
1.7107-1.74360.37581420.350434283570100
1.7436-1.77920.33611400.323634513591100
1.7792-1.81790.32381430.310834863629100
1.8179-1.86020.3371390.290834583597100
1.8602-1.90670.33561450.286335023647100
1.9067-1.95820.26361450.271234313576100
1.9582-2.01590.2861450.241934573602100
2.0159-2.08090.24121470.225434753622100
2.0809-2.15530.21971410.213734903631100
2.1553-2.24160.22351390.211534293568100
2.2416-2.34360.19711460.206834883634100
2.3436-2.46710.25671440.206934493593100
2.4671-2.62170.21111440.203434583602100
2.6217-2.82410.24331420.204534863628100
2.8241-3.10820.21741470.198934563603100
3.1082-3.55780.20751410.171334543595100
3.5578-4.48160.19571440.151434703614100
4.4816-42.31680.17371430.167234733616100

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