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- PDB-4g36: Photinus pyralis luciferase in the adenylate-forming conformation... -

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Basic information

Entry
Database: PDB / ID: 4g36
TitlePhotinus pyralis luciferase in the adenylate-forming conformation bound to DLSA
ComponentsLuciferin 4-monooxygenase
KeywordsLIGASE / ANL Superfamily / adenylating enzymes / luciferase / domain alternation / firefly 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
Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / 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 ...Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / 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 / AMP-binding enzyme, C-terminal domain superfamily / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE / Luciferin 4-monooxygenase
Similarity search - Component
Biological speciesPhotinus pyralis (common eastern firefly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.624 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 1.1Sep 5, 2012Group: Derived calculations
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Sep 13, 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 / 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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)123,6744
Polymers122,4612
Non-polymers1,2132
Water1,29772
1
A: Luciferin 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8372
Polymers61,2301
Non-polymers6071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Luciferin 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8372
Polymers61,2301
Non-polymers6071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.040, 93.040, 297.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Luciferin 4-monooxygenase / Luciferase


Mass: 61230.406 Da / Num. of mol.: 2
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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 300 mM Na/K Tartrate, 20% PEG 6000, 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2006
RadiationMonochromator: SSRL 9-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.62→70 Å / Num. all: 45768 / Num. obs: 45585 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.6
Reflection shellResolution: 2.62→2.77 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 5.9 / Num. unique all: 6554 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_837)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D1S

2d1s


Resolution: 2.624→54.664 Å / σ(F): 1.45 / Phase error: 25.97 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 2311 5.07 %Random
Rwork0.1868 ---
all0.1893 45830 --
obs0.1893 45569 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.319 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.379 Å2-0 Å20 Å2
2---2.379 Å2-0 Å2
3---4.7579 Å2
Refinement stepCycle: LAST / Resolution: 2.624→54.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8070 0 80 72 8222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088335
X-RAY DIFFRACTIONf_angle_d1.16811345
X-RAY DIFFRACTIONf_dihedral_angle_d15.0272965
X-RAY DIFFRACTIONf_chiral_restr0.0721302
X-RAY DIFFRACTIONf_plane_restr0.0051461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.624-2.68110.27511450.23882676X-RAY DIFFRACTION94
2.6811-2.74340.27251430.23982633X-RAY DIFFRACTION94
2.7434-2.8120.31391450.2362660X-RAY DIFFRACTION94
2.812-2.88810.28581320.23012687X-RAY DIFFRACTION95
2.8881-2.9730.27961320.22512662X-RAY DIFFRACTION95
2.973-3.0690.28061510.21132652X-RAY DIFFRACTION94
3.069-3.17870.26241370.20922675X-RAY DIFFRACTION95
3.1787-3.30590.27871520.20292665X-RAY DIFFRACTION94
3.3059-3.45640.2641520.19572694X-RAY DIFFRACTION94
3.4564-3.63860.23071140.18452700X-RAY DIFFRACTION96
3.6386-3.86650.23941300.17122743X-RAY DIFFRACTION95
3.8665-4.16490.18461460.15672692X-RAY DIFFRACTION95
4.1649-4.58380.19481390.152734X-RAY DIFFRACTION95
4.5838-5.24670.20061650.15492729X-RAY DIFFRACTION94
5.2467-6.60840.23941660.19192769X-RAY DIFFRACTION94
6.6084-54.67540.21741540.17452891X-RAY DIFFRACTION93

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