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- PDB-5lq4: The Structure of ThcOx, the First Oxidase Protein from the Cyanob... -

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Basic information

Entry
Database: PDB / ID: 5lq4
TitleThe Structure of ThcOx, the First Oxidase Protein from the Cyanobactin Pathways
Components(CyaGox) x 2
KeywordsOXIDOREDUCTASE / Cyanobactins Oxidase S-SAD RIPPs
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
ThcOx helix turn helix domain / : / ThcOx helix turn helix domain / Cyanobactin oxidase ThcOx, / SagB-type dehydrogenase domain / : / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family ...ThcOx helix turn helix domain / : / ThcOx helix turn helix domain / Cyanobactin oxidase ThcOx, / SagB-type dehydrogenase domain / : / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / SagB-type dehydrogenase domain protein
Similarity search - Component
Biological speciesCyanothece sp.
Cyanothece sp. PCC 7425 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsBent, A.F. / Wagner, A. / Naismith, J.H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K015508/1 United Kingdom
European Research Council339367 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Structure of the cyanobactin oxidase ThcOx from Cyanothece sp. PCC 7425, the first structure to be solved at Diamond Light Source beamline I23 by means of S-SAD.
Authors: Bent, A.F. / Mann, G. / Houssen, W.E. / Mykhaylyk, V. / Duman, R. / Thomas, L. / Jaspars, M. / Wagner, A. / Naismith, J.H.
History
DepositionAug 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CyaGox
B: CyaGox
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,2244
Polymers105,3112
Non-polymers9132
Water724
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10480 Å2
ΔGint-44 kcal/mol
Surface area39150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.300, 109.300, 195.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 3 - 468

Dom-IDAuth asym-IDLabel asym-IDLabel seq-ID
1AA1 - 466
2BB3 - 468

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Components

#1: Protein CyaGox


Mass: 52297.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece sp. (strain PCC 7425 / ATCC 29141) (bacteria)
Strain: PCC 7425 / ATCC 29141 / Gene: Cyan7425_0520 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: B8HTZ1
#2: Protein CyaGox


Mass: 53013.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece sp. (strain PCC 7425 / ATCC 29141) (bacteria)
Strain: PCC 7425 / ATCC 29141 / Gene: Cyan7425_0520 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: B8HTZ1
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C17H21N4O9P / Source: (gene. exp.) Cyanothece sp. PCC 7425 (bacteria) / Strain: PCC 7425 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: 6,7-dihydropteridine reductase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.6553.65Two molecules per asymmetric unit.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop7.751.0 M sodium citrate, 0.1 M CHES pH 7.75
2932vapor diffusion7.751.0 M sodium citrate, 0.1 M CHES pH 7.75

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDAmbient temp details
11001
2502An accurate temperature calibration is still outstanding; this value is based on a temperature of 44 K at the goniometer head assuming a temperature rise of around 6 K through the sample mount
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0311.7712
SYNCHROTRONDiamond I2323.0955
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 S 6M1PIXELApr 20, 2015
DECTRIS PILATUS 12M2PIXELFeb 29, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.77121
23.09551
Reflection

Biso Wilson estimate: 60.235 Å2 / Entry-ID: 5LQ4

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2.65-72.84352041008.10.083117.9
3.15-217.5557502091.625.8228.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.65-2.728.50.8362.7199.6
3.15-3.37252.3280.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→72.83 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 23.318 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.722 / ESU R Free: 0.289 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22838 1751 5 %RANDOM
Rwork0.19664 ---
obs0.19815 33383 99.92 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 74.681 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.65→72.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7344 0 0 4 7348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197527
X-RAY DIFFRACTIONr_bond_other_d0.0030.027188
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.98310277
X-RAY DIFFRACTIONr_angle_other_deg1.056316555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7115920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04724.308325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.562151244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4591538
X-RAY DIFFRACTIONr_chiral_restr0.0710.21193
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218365
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021655
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_it2.9194.4093686
X-RAY DIFFRACTIONr_mcbond_other2.9194.4093685
X-RAY DIFFRACTIONr_mcangle_it4.7556.6134601
X-RAY DIFFRACTIONr_mcangle_other4.7556.6144602
X-RAY DIFFRACTIONr_scbond_it3.2184.7273841
X-RAY DIFFRACTIONr_scbond_other3.2174.7273840
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1996.9675676
X-RAY DIFFRACTIONr_long_range_B_refined7.6735.2288081
X-RAY DIFFRACTIONr_long_range_B_other7.6735.238082
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 54310 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 113 -
Rwork0.283 2423 -
obs--99.96 %
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)
15.6795-2.9763-5.12135.02092.262911.65110.05640.3482-0.0201-0.5557-0.4481-0.88920.21341.04870.39170.43220.0775-0.02440.58540.17820.5602130.923140.4926.648
21.1991-0.48160.28141.2232-3.10739.3458-0.10850.24790.2504-0.1581-0.057-0.03210.33320.02440.16540.25930.0005-0.06360.27580.06720.3395120.434140.82635.768
36.2596-2.17030.31713.70750.70933.9041-0.1783-0.37930.00460.37330.2380.4867-0.2195-0.3615-0.05970.20720.0992-0.06290.30530.01290.3117113.718140.64952.565
43.87730.01160.27652.14580.0352.33540.07-0.1864-0.13080.14420.0363-0.25440.0840.2338-0.10620.01780.009-0.01410.0833-0.07290.1593152.898118.36662.791
54.65072.0323-2.92079.4454-4.29097.82490.14750.0232-0.20840.0437-0.1109-0.4315-0.03570.0144-0.03660.12010.039-0.04930.2369-0.04720.2788124.947143.39783.411
61.4352-0.3281-0.66191.36090.382911.320.0268-0.2182-0.29050.28170.0438-0.00270.93490.1006-0.07060.1471-0.005-0.02910.1933-0.02290.321124.487142.29489.678
73.1888-0.31950.63836.6141.92027.68270.2090.0810.4865-0.52410.0206-0.3756-0.84380.3316-0.22960.18950.04710.05230.218-0.0710.2912131.099150.02764.711
82.86790.3560.19233.22791.17362.3657-0.01990.2829-0.3422-0.12720.04980.15250.3568-0.2138-0.02990.0924-0.0555-0.03840.0996-0.06640.2314137.547108.68648.644
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 36
2X-RAY DIFFRACTION2A37 - 135
3X-RAY DIFFRACTION3A136 - 207
4X-RAY DIFFRACTION4A208 - 472
5X-RAY DIFFRACTION5B1 - 17
6X-RAY DIFFRACTION6B18 - 102
7X-RAY DIFFRACTION7B103 - 207
8X-RAY DIFFRACTION8B208 - 473

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