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- PDB-5d9d: Luciferin-regenerating enzyme solved by SAD using synchrotron rad... -

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Basic information

Entry
Database: PDB / ID: 5d9d
TitleLuciferin-regenerating enzyme solved by SAD using synchrotron radiation at room 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 / SAD / Resolution: 1.701 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 1.1Feb 19, 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 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)34,9466
Polymers34,2021
Non-polymers7445
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-85 kcal/mol
Surface area12710 Å2
Unit cell
Length a, b, c (Å)48.107, 77.177, 84.916
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-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30.6% PEG 3350, 10% MPD, 0.1M MOPS pH 7.0, 0.2M MgCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9839 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 1, 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: 1.7→48.1 Å / Num. obs: 67034 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 16.84 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.101 / Χ2: 1.143 / Net I/σ(I): 10.58 / Num. measured all: 258663
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.80.6960.6252.154103710868107970.72899.3
1.8-1.930.8650.3863.483915110206102030.449100
1.93-2.080.9490.2295.8836521947094640.26799.9
2.08-2.280.9730.1588.3833874874987420.18399.9
2.28-2.550.9820.12410.6930638789578890.14499.9
2.55-2.940.9910.08514.6727123697469690.09999.9
2.94-3.60.9960.05321.922809587658750.062100
3.6-5.070.9970.03928.5117682456245590.04599.9
5.070.9980.03630.139828253925360.04299.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.701→41.857 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1776 2664 3.97 %
Rwork0.1444 64365 -
obs0.1457 67029 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.35 Å2 / Biso mean: 23.3395 Å2 / Biso min: 7.97 Å2
Refinement stepCycle: final / Resolution: 1.701→41.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 12 158 2551
Biso mean--42.48 34.98 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192528
X-RAY DIFFRACTIONf_angle_d1.7783449
X-RAY DIFFRACTIONf_chiral_restr0.119389
X-RAY DIFFRACTIONf_plane_restr0.011443
X-RAY DIFFRACTIONf_dihedral_angle_d13.73931
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7006-1.73150.23251460.22093327347398
1.7315-1.76480.22051300.215733963526100
1.7648-1.80090.24921380.197433933531100
1.8009-1.840.2491390.190634233562100
1.84-1.88280.19621480.178933803528100
1.8828-1.92990.23041320.1633903522100
1.9299-1.98210.17871500.150433793529100
1.9821-2.04040.16221420.142133503492100
2.0404-2.10630.16441380.133334093547100
2.1063-2.18150.17381330.136634223555100
2.1815-2.26890.16071470.130233923539100
2.2689-2.37210.15971350.136633863521100
2.3721-2.49720.19271460.143433843530100
2.4972-2.65360.20361430.145633913534100
2.6536-2.85840.16491310.142133903521100
2.8584-3.1460.17471480.141533793527100
3.146-3.6010.17151350.127733853520100
3.601-4.53610.14581430.121234003543100
4.5361-41.86940.17351400.146933893529100
Refinement TLS params.Method: refined / Origin x: 34.3234 Å / Origin y: 14.3531 Å / Origin z: 17.1553 Å
111213212223313233
T0.0775 Å20.0059 Å2-0.0038 Å2-0.0954 Å20.007 Å2--0.0926 Å2
L0.3147 °2-0.0758 °20.0496 °2-0.7441 °2-0.1633 °2--0.7617 °2
S-0.0406 Å °-0.0332 Å °-0.0331 Å °0.0474 Å °0.0191 Å °-0.0064 Å °-0.0236 Å °0.0343 Å °-0.0002 Å °
Refinement TLS groupSelection details: ALL

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