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- PDB-5d9b: Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined... -

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Basic information

Entry
Database: PDB / ID: 5d9b
TitleLuciferin-regenerating enzyme solved by SIRAS using XFEL (refined against native data)
ComponentsLuciferin regenerating enzyme
KeywordsHYDROLASE / beta-prooeller
Function / homology
Function and homology information


gluconolactonase / 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
Biological speciesPhotinus pyralis (common eastern firefly)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / SIRAS / Resolution: 1.5 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

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Assembly

Deposited unit
A: Luciferin regenerating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3443
Polymers34,2021
Non-polymers1422
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-24 kcal/mol
Surface area12640 Å2
Unit cell
Length a, b, c (Å)48.210, 77.590, 84.760
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
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: 0.981 Å
DetectorType: MPCCD / Detector: CCD / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 1.5→10 Å / Num. obs: 51698 / % possible obs: 100 % / Redundancy: 222.2 % / Net I/σ(I): 2.56

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
PDB_EXTRACT3.15data extraction
SHELXDEphasing
CrystFELdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 1.5→9.998 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 2060 4.01 %
Rwork0.1845 49358 -
obs0.1864 51418 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.7 Å2 / Biso mean: 27.9384 Å2 / Biso min: 12.51 Å2
Refinement stepCycle: final / Resolution: 1.5→9.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 9 188 2582
Biso mean--32.61 39.85 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112498
X-RAY DIFFRACTIONf_angle_d1.3463408
X-RAY DIFFRACTIONf_chiral_restr0.069383
X-RAY DIFFRACTIONf_plane_restr0.007439
X-RAY DIFFRACTIONf_dihedral_angle_d13.38921
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.53480.3741390.335732083347
1.5348-1.5730.35431340.322232553389
1.573-1.61540.31371340.296332433377
1.6154-1.66270.29431370.283332823419
1.6627-1.71610.28841360.252832323368
1.7161-1.77710.28721340.23332613395
1.7771-1.84780.28511390.215732773416
1.8478-1.93140.25191320.194232473379
1.9314-2.03240.1971390.178532913430
2.0324-2.15850.21011370.161732763413
2.1585-2.32330.20871350.1632913426
2.3233-2.55350.18491400.166333253465
2.5535-2.9150.22611380.174133133451
2.915-3.64280.22371400.166633803520
3.6428-9.99870.22311460.166634773623
Refinement TLS params.Method: refined / Origin x: 34.2888 Å / Origin y: 14.5862 Å / Origin z: 17.5935 Å
111213212223313233
T0.1244 Å20.0065 Å2-0.0094 Å2-0.142 Å20.0019 Å2--0.1407 Å2
L0.6909 °2-0.045 °2-0.1285 °2-1.1919 °2-0.2021 °2--1.4282 °2
S-0.0458 Å °-0.1019 Å °-0.005 Å °0.0979 Å °0.0266 Å °-0.0045 Å °-0.0247 Å °0.0202 Å °0.018 Å °
Refinement TLS groupSelection details: ALL

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