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- PDB-5gyz: luciferase AMP/7-cy-L complex -

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Basic information

Entry
Database: PDB / ID: 5gyz
Titleluciferase AMP/7-cy-L complex
ComponentsLuciferin 4-monooxygenase
KeywordsOXIDOREDUCTASE / Substrate / Luciferase
Function / homology
Function and homology information


Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity / firefly luciferase / bioluminescence / peroxisome / protein-folding chaperone binding / ATP binding / metal ion binding
Similarity search - Function
ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7BV / ADENOSINE MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / Luciferin 4-monooxygenase
Similarity search - Component
Biological speciesPhotinus pyralis (common eastern firefly)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSu, J. / Wang, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Program on Key Basic Research Project of China2013CB734002 China
CitationJournal: To Be Published
Title: Structure of luciferase with AMP/7-cy-L at 2.4 Angstroms resolution
Authors: Chao, T.Z. / Su, J.
History
DepositionSep 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5097
Polymers48,4181
Non-polymers1,0916
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint1 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.443, 73.443, 96.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Luciferin 4-monooxygenase / Luciferase


Mass: 48417.523 Da / Num. of mol.: 1 / Fragment: UNP residues 4-438
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photinus pyralis (common eastern firefly)
Production host: Escherichia coli (E. coli) / References: UniProt: P08659, firefly luciferase

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Non-polymers , 5 types, 227 molecules

#2: Chemical ChemComp-7BV / (4S)-2-[6-(azepan-1-yl)-1,3-benzothiazol-2-yl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid


Mass: 361.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N3O2S2
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 293 K / Method: evaporation / Details: Sodium malonate, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 19770 / % possible obs: 98.9 % / Redundancy: 7.4 % / Net I/σ(I): 47.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BA3

1ba3


Resolution: 2.4→40.2 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.82
RfactorNum. reflection% reflection
Rfree0.227 1016 5.14 %
Rwork0.173 --
obs0.176 19765 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→40.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 71 221 3681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093544
X-RAY DIFFRACTIONf_angle_d1.084797
X-RAY DIFFRACTIONf_dihedral_angle_d14.4922112
X-RAY DIFFRACTIONf_chiral_restr0.06526
X-RAY DIFFRACTIONf_plane_restr0.006612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4013-2.52790.31151550.23142649X-RAY DIFFRACTION98
2.5279-2.68630.28351410.21132629X-RAY DIFFRACTION99
2.6863-2.89360.2831590.20612652X-RAY DIFFRACTION99
2.8936-3.18470.29041340.20072691X-RAY DIFFRACTION99
3.1847-3.64530.2731420.18292688X-RAY DIFFRACTION99
3.6453-4.59160.20181160.14592718X-RAY DIFFRACTION99
4.5916-40.20580.15441690.14742722X-RAY DIFFRACTION100

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