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- PDB-1brl: THREE-DIMENSIONAL STRUCTURE OF BACTERIAL LUCIFERASE FROM VIBRIO H... -

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Basic information

Entry
Database: PDB / ID: 1brl
TitleTHREE-DIMENSIONAL STRUCTURE OF BACTERIAL LUCIFERASE FROM VIBRIO HARVEYI AT 2.4 ANGSTROMS RESOLUTION
Components(BACTERIAL LUCIFERASE) x 2
KeywordsLUMINESCENCE / MONOOXYGENASE
Function / homology
Function and homology information


bacterial luciferase / alkanal monooxygenase (FMN-linked) activity / bioluminescence / cytosol
Similarity search - Function
Alkanal monooxygenase / Bacterial luciferase, conserved site / Bacterial luciferase subunits signature. / Bacterial luciferase/NFP / : / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel ...Alkanal monooxygenase / Bacterial luciferase, conserved site / Bacterial luciferase subunits signature. / Bacterial luciferase/NFP / : / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Alkanal monooxygenase beta chain / Alkanal monooxygenase alpha chain
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsFisher, A.J. / Rayment, I.
CitationJournal: Biochemistry / Year: 1995
Title: Three-dimensional structure of bacterial luciferase from Vibrio harveyi at 2.4 A resolution.
Authors: Fisher, A.J. / Raushel, F.M. / Baldwin, T.O. / Rayment, I.
History
DepositionMar 20, 1995Processing site: BNL
Revision 1.0Apr 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: BACTERIAL LUCIFERASE
B: BACTERIAL LUCIFERASE
C: BACTERIAL LUCIFERASE
D: BACTERIAL LUCIFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,2585
Polymers153,1634
Non-polymers951
Water1,31573
1
A: BACTERIAL LUCIFERASE
B: BACTERIAL LUCIFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6773
Polymers76,5822
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-29 kcal/mol
Surface area26550 Å2
MethodPISA
2
C: BACTERIAL LUCIFERASE
D: BACTERIAL LUCIFERASE


Theoretical massNumber of molelcules
Total (without water)76,5822
Polymers76,5822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-22 kcal/mol
Surface area26600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.900, 112.700, 301.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.87049, 0.41921, 0.2579), (0.35359, -0.16813, -0.92017), (-0.34239, 0.89218, -0.29458)
Vector: -55.857, 172.442, 239.19501)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 1 .. A 355 .. M1 B 1 .. B 319 ..

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Components

#1: Protein BACTERIAL LUCIFERASE


Mass: 40197.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: APO (NO FMN) / Source: (natural) Vibrio harveyi (bacteria) / References: UniProt: P07740, bacterial luciferase
#2: Protein BACTERIAL LUCIFERASE


Mass: 36384.684 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: APO (NO FMN) / Source: (natural) Vibrio harveyi (bacteria) / References: UniProt: P07739, bacterial luciferase
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 63 %
Crystal
*PLUS
Density % sol: 61.5 %
Crystal grow
*PLUS
pH: 5.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlluciferase1drop
21.4 Mammonium sulfate1reservoir
3200 mM1reservoirNaH2PO4
4100 mMsuccinate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.908
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Oct 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionRedundancy: 3.9 % / Rmerge(I) obs: 0.115
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 74342 / % possible obs: 92 % / Num. measured all: 290488 / Rmerge(I) obs: 0.115

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Processing

Software
NameVersionClassification
TNTrefinement
PURDUE(OSC)data reduction
RefinementResolution: 2.4→30 Å / σ(F): 0 /
RfactorNum. reflection
obs0.208 74306
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10354 0 5 146 10505
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.715
X-RAY DIFFRACTIONt_dihedral_angle_d20.193
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.006
X-RAY DIFFRACTIONt_gen_planes0.008
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.193

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