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- PDB-5gtq: Luciferin-regenerating enzyme at cryogenic temperature -

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Basic information

Entry
Database: PDB / ID: 5gtq
TitleLuciferin-regenerating enzyme at cryogenic temperature
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: 1.13 Å
AuthorsYamashita, K. / Murai, T. / Yamamoto, M. / Gomi, K. / Kajiyama, N. / Kato, H. / Nakatsu, T.
CitationJournal: To Be Published
Title: Luciferin-regenerating enzyme at cryogenic temperature
Authors: Yamashita, K.
History
DepositionAug 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
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
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 / _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)34,9567
Polymers34,2021
Non-polymers7546
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-55 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.275, 76.696, 83.980
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, 398 molecules

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


Mass: 200.590 Da / Num. of mol.: 2 / 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.: 392 / 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 GENEBANK 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: 2.23 Å3/Da / Density % sol: 44.74 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / 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 (28.4% PEG3350, 10% MPD, 0.1 M MOPS pH 7.0, 0.2 M MgCl2) at 1:1 ratio

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9839 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 17, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9839 Å / Relative weight: 1
ReflectionResolution: 1.13→36.831 Å / Num. obs: 216478 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.53 % / Biso Wilson estimate: 8.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Net I/σ(I): 18.27
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.13-1.20.2563.390.888189.9
1.2-1.280.2135.730.95199.4
1.28-1.380.1538.110.975199.7
1.38-1.520.112.250.989199.8
1.52-1.690.06418.620.995199.8
1.69-1.960.04227.950.998199.6
1.96-2.390.0339.370.998199.3
2.39-3.380.02347.770.999199.5
3.38-36.8310.01856.120.999199.3

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Processing

Software
NameVersionClassification
XDSJanuary 10, 2014data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5D9C

5d9c


Resolution: 1.13→36.831 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.61
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.1389 8640 3.99 %
Rwork0.1188 --
obs0.1195 216476 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 49.73 Å2 / Biso mean: 13.7035 Å2 / Biso min: 5.48 Å2
Refinement stepCycle: final / Resolution: 1.13→36.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 25 392 2802
Biso mean--18.31 26.69 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062609
X-RAY DIFFRACTIONf_angle_d0.9953582
X-RAY DIFFRACTIONf_chiral_restr0.094399
X-RAY DIFFRACTIONf_plane_restr0.007464
X-RAY DIFFRACTIONf_dihedral_angle_d17.114984
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1302-1.14310.17162360.17175588582480
1.1431-1.15650.17352330.16266112634585
1.1565-1.17060.18422710.15476529680092
1.1706-1.18550.15112840.1486752703695
1.1855-1.20110.14132970.13286881717898
1.2011-1.21750.13792920.12377039733199
1.2175-1.23490.13322970.11970427339100
1.2349-1.25330.13372960.1177012730899
1.2533-1.27290.1212880.11577016730499
1.2729-1.29380.13332950.11870197314100
1.2938-1.31610.16612950.118170627357100
1.3161-1.340.1452930.111970517344100
1.34-1.36580.14092980.107270217319100
1.3658-1.39370.12912950.099770717366100
1.3937-1.4240.1232900.094870277317100
1.424-1.45710.12362920.097370387330100
1.4571-1.49360.11692960.093870617357100
1.4936-1.5340.12332910.094770547345100
1.534-1.57910.12442960.093771247420100
1.5791-1.63010.12412920.096470227314100
1.6301-1.68830.12172960.096170437339100
1.6883-1.75590.12382900.102970197309100
1.7559-1.83580.13142860.104670767362100
1.8358-1.93260.1112970.106269957292100
1.9326-2.05370.12852950.10937063735899
2.0537-2.21220.13542840.11526998728299
2.2122-2.43480.13852910.1247011730299
2.4348-2.7870.16892910.13767057734899
2.787-3.51090.15582920.134870297321100
3.5109-36.85090.14452910.13457024731599

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