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- PDB-3rao: Crystal Structure of the Luciferase-like Monooxygenase from Bacil... -

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Basic information

Entry
Database: PDB / ID: 3rao
TitleCrystal Structure of the Luciferase-like Monooxygenase from Bacillus cereus ATCC 10987.
ComponentsPutative Luciferase-like Monooxygenase
KeywordsStructural Genomics / Unknown function / unknown / PSI-Biology / Midwest Center for Structural Genomics / MCSG / enzyme
Function / homologyLuciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Bacterial luciferase family protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsDomagalski, M.J. / Chruszcz, M. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Luciferase-like Monooxygenase from Bacillus cereus ATCC 10987.
Authors: Domagalski, M.J. / Chruszcz, M. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W.
History
DepositionMar 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Putative Luciferase-like Monooxygenase
B: Putative Luciferase-like Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,94412
Polymers84,9832
Non-polymers96110
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative Luciferase-like Monooxygenase
hetero molecules

A: Putative Luciferase-like Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,94412
Polymers84,9832
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_564-x+y,-x+1,z-1/31
Buried area5190 Å2
ΔGint-159 kcal/mol
Surface area28810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.807, 126.807, 124.234
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A0 - 348
2114B0 - 348

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Components

#1: Protein Putative Luciferase-like Monooxygenase


Mass: 42491.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: BCE_1067 / Plasmid: p15Tvlic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIPL / References: UniProt: Q73CJ8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 3.39 Å3/Da / Density % sol: 63.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M NaHepes, pH 7.5, 4%PEG400, 2M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2010
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 50096 / Num. obs: 50096 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 25.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2529 / Rsym value: 0.66 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
DMmodel building
MLPHAREphasing
CCP4model building
RESOLVEmodel building
ARP/wARPmodel building
REFMAC5.6.0070refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
DMphasing
CCP4phasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.857 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20994 2536 5.1 %RANDOM
Rwork0.16775 ---
all0.16987 47374 --
obs0.16987 47374 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.199 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0.19 Å20 Å2
2---0.38 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5474 0 50 285 5809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225651
X-RAY DIFFRACTIONr_bond_other_d0.0110.023807
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9567661
X-RAY DIFFRACTIONr_angle_other_deg0.91139266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9675690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20224.354271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5215964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4481534
X-RAY DIFFRACTIONr_chiral_restr0.0870.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021149
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4489 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.430.5
medium thermal3.842
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 177 -
Rwork0.248 3511 -
obs--98.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3746-0.18260.10.1522-0.11310.34070.0363-0.0032-0.00680.0823-0.01250.03360.0212-0.1341-0.02370.27410.01870.03940.32940.00160.0483-6.72377.274-4.405
20.2193-0.00510.35580.26320.14670.7343-0.0278-0.0417-0.0040.02040.05970.00410.0076-0.049-0.03190.2574-0.01260.0270.30540.01070.0526-1.16570.246-2.264
30.92210.08950.92120.78350.43641.1538-0.01390.0407-0.0619-0.05310.1211-0.15310.1040.152-0.10720.26670.04890.04920.36210.03840.06215.72863.5311.962
40.9980.31280.55350.6962-0.01630.38860.0172-0.20060.11060.0205-0.05820.0869-0.038-0.0990.0410.3020.01240.04230.3305-0.02750.0224-8.18180.015-3.443
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 19
2X-RAY DIFFRACTION1B-2 - 19
3X-RAY DIFFRACTION2A20 - 127
4X-RAY DIFFRACTION2B20 - 132
5X-RAY DIFFRACTION3A128 - 200
6X-RAY DIFFRACTION3B133 - 194
7X-RAY DIFFRACTION4A201 - 348
8X-RAY DIFFRACTION4B195 - 348

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