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- PDB-4g37: Structure of cross-linked firefly luciferase in second catalytic ... -

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Basic information

Entry
Database: PDB / ID: 4g37
TitleStructure of cross-linked firefly luciferase in second catalytic conformation
ComponentsLuciferin 4-monooxygenase
KeywordsLIGASE / ANL Superfamily / adenylating enzymes / luciferase / domain alternation / trapped conformation / chemical cross-linker
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, C-terminal domain / 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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme ...ANL, C-terminal domain / 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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE / 4,4'-(ethylenediimino)bis[4-oxobutyrate] / Luciferin 4-monooxygenase
Similarity search - Component
Biological speciesPhotinus pyralis (common eastern firefly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.396 Å
AuthorsSundlov, J.A. / Branchini, B.R. / Gulick, A.M.
CitationJournal: Biochemistry / Year: 2012
Title: Crystal structure of firefly luciferase in a second catalytic conformation supports a domain alternation mechanism.
Authors: Sundlov, J.A. / Fontaine, D.M. / Southworth, T.L. / Branchini, B.R. / Gulick, A.M.
History
DepositionJul 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Luciferin 4-monooxygenase
B: Luciferin 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,21411
Polymers122,0322
Non-polymers2,1819
Water3,423190
1
A: Luciferin 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0895
Polymers61,0161
Non-polymers1,0734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Luciferin 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1256
Polymers61,0161
Non-polymers1,1085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.638, 184.091, 170.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Luciferin 4-monooxygenase / Luciferase


Mass: 61016.133 Da / Num. of mol.: 2
Mutation: C82S, I108C, T214A, A215L, C216A, I232A, C258S, F295L, E354K, C391S, Y447C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photinus pyralis (common eastern firefly)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P08659, firefly luciferase

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Non-polymers , 5 types, 199 molecules

#2: Chemical ChemComp-SLU / 5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE


Mass: 606.611 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H18N8O8S3
#3: Chemical ChemComp-XLX / 4,4'-(ethylenediimino)bis[4-oxobutyrate] / 1,2-bis(maleimido)ethane, hydrolyzed open form


Mass: 274.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N2O6
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30 % PEG 4000, 50 mM NaCl, 50 mM HEPPS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 13, 2012 / Details: SSRL BL 9-2
RadiationMonochromator: SSRL BL 9-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.396→30 Å / Num. all: 47067 / Num. obs: 44431 / % possible obs: 94.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.3
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 3.8 / % possible all: 82.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_837)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LCI
Resolution: 2.396→29.219 Å / SU ML: 0.65 / σ(F): 1.35 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 2274 5.12 %
Rwork0.1993 --
obs0.2023 44395 94.13 %
all-47163 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.659 Å2 / ksol: 0.27 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.0527 Å2-0 Å20 Å2
2---7.7222 Å2-0 Å2
3---14.7749 Å2
Refinement stepCycle: LAST / Resolution: 2.396→29.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8084 0 121 190 8395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088389
X-RAY DIFFRACTIONf_angle_d1.15511428
X-RAY DIFFRACTIONf_dihedral_angle_d13.8352965
X-RAY DIFFRACTIONf_chiral_restr0.0741309
X-RAY DIFFRACTIONf_plane_restr0.0061469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3959-2.4480.33091180.2522022X-RAY DIFFRACTION73
2.448-2.50490.3511190.25522360X-RAY DIFFRACTION85
2.5049-2.56750.36481300.2532524X-RAY DIFFRACTION92
2.5675-2.63690.34841520.23682582X-RAY DIFFRACTION94
2.6369-2.71440.31451640.22242621X-RAY DIFFRACTION95
2.7144-2.80190.28421450.21192647X-RAY DIFFRACTION96
2.8019-2.9020.30121430.19982697X-RAY DIFFRACTION97
2.902-3.01810.2671470.21472732X-RAY DIFFRACTION98
3.0181-3.15530.30731430.21422724X-RAY DIFFRACTION98
3.1553-3.32140.33731430.23432740X-RAY DIFFRACTION99
3.3214-3.52920.27011460.21652725X-RAY DIFFRACTION98
3.5292-3.80120.23321460.19532742X-RAY DIFFRACTION97
3.8012-4.18270.22531390.17152692X-RAY DIFFRACTION96
4.1827-4.78560.19561430.15822685X-RAY DIFFRACTION95
4.7856-6.02070.23161470.19032757X-RAY DIFFRACTION97
6.0207-29.22130.2071490.18152871X-RAY DIFFRACTION96

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