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- PDB-5hi8: Structure of T-type Phycobiliprotein Lyase CpeT from Prochlorococ... -

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Basic information

Entry
Database: PDB / ID: 5hi8
TitleStructure of T-type Phycobiliprotein Lyase CpeT from Prochlorococcus phage P-HM1
ComponentsAntenna proteinLight-harvesting complexes of green plants
KeywordsLYASE / beta barrel
Function / homologyChromophore lyase CpcT/CpeT / Chromophore lyase CpcT/CpeT superfamily / CpeT/CpcT family (DUF1001) / protein-phycocyanobilin linkage / lyase activity / ACETATE ION / Antenna protein
Function and homology information
Biological speciesProchlorococcus phage P-HM1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsGasper, R. / Schwach, J. / Frankenberg-Dinkel, N. / Hofmann, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
Funded by Transfer.NRW: Science-to-Business Pre Seed300271002 Germany
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Distinct Features of Cyanophage-encoded T-type Phycobiliprotein Lyase Phi CpeT: THE ROLE OF AUXILIARY METABOLIC GENES.
Authors: Gasper, R. / Schwach, J. / Hartmann, J. / Holtkamp, A. / Wiethaus, J. / Riedel, N. / Hofmann, E. / Frankenberg-Dinkel, N.
History
DepositionJan 11, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: Antenna protein
B: Antenna protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6865
Polymers32,5782
Non-polymers1083
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-16 kcal/mol
Surface area14800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.290, 61.680, 93.340
Angle α, β, γ (deg.)90.000, 109.770, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq -1:134 ) and (not element H)
21chain B and (resseq -1:134 ) and (not element H)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 0 / Label seq-ID: 2

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq -1:134 ) and (not element H)AA
2chain B and (resseq -1:134 ) and (not element H)BB

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Components

#1: Protein Antenna protein / Light-harvesting complexes of green plants / CpeT


Mass: 16289.001 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus phage P-HM1 (virus) / Gene: cpeT, PHM1_028 / Plasmid: pASK-IBA45plus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E3SMK9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.1 M Glycine, 0.05 M MgAcetate, 32 % PEG 400, pH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00005 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2015
RadiationMonochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 60405 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.53 % / Biso Wilson estimate: 35.27 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.37
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.8-1.850.9541.18195.7
1.85-1.90.7211.6196.7
1.9-1.950.4982.22196.7
1.95-2.010.3822.93197
2.01-2.080.2953.52197.9
2.08-2.150.2484.19197.9
2.15-2.230.1935.19197.6
2.23-2.320.1766.04198.3
2.32-2.430.1496.79198.3
2.43-2.550.1267.66198.3
2.55-2.680.119.4198.6
2.68-2.850.09711.02198.3
2.85-3.040.08312.31198.9
3.04-3.290.07513.26199.1
3.29-3.60.07215.13199
3.6-4.020.0715.94198.7
4.02-4.650.06716.15199.3
4.65-5.690.06916.54199.3
5.69-8.050.07116.26199.5
8.050.07116.58199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.81 Å43.95 Å
Translation5.81 Å43.95 Å

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Processing

Software
NameVersionClassification
PHENIX1-9-1692refinement
XSCALENovember 3, 2014data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O4O

4o4o


Resolution: 1.8→43.918 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 29.7
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 3027 5.02 %Random selection
Rwork0.2071 ---
obs0.2082 60319 97.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.9 Å2 / Biso mean: 59.5374 Å2 / Biso min: 31.01 Å2
Refinement stepCycle: final / Resolution: 1.8→43.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 9 77 2392
Biso mean--55.63 47.82 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072398
X-RAY DIFFRACTIONf_angle_d1.0883255
X-RAY DIFFRACTIONf_chiral_restr0.046308
X-RAY DIFFRACTIONf_plane_restr0.005419
X-RAY DIFFRACTIONf_dihedral_angle_d14.713842
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1153X-RAY DIFFRACTIONPOSITIONAL0.015
12B1153X-RAY DIFFRACTIONPOSITIONAL0.015
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.86430.37842950.37445671596696
1.8643-1.93890.3442980.32385608590696
1.9389-2.02720.28813000.26195676597697
2.0272-2.13410.29833010.25425707600898
2.1341-2.26780.26773010.22735751605298
2.2678-2.44290.25393040.23155761606598
2.4429-2.68870.29973040.22955714601898
2.6887-3.07760.25553060.23375771607799
3.0776-3.87710.2383100.19415829613999
3.8771-43.93110.16023080.16645804611299
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)
14.1534-1.31750.51494.16740.46481.68070.7058-1.14551.13581.0953-0.1725-1.0307-0.93641.2396-0.47160.5224-0.1563-0.02650.7638-0.15140.424765.292823.861830.1048
26.9231.1116-2.25613.06970.01762.7020.02530.38820.09850.14090.1497-0.21010.15420.6172-0.44580.44930.02070.02520.49450.02050.394268.955919.28919.3458
39.1993-3.1612-4.57327.85332.89427.29830.3070.34360.3698-0.3967-0.1398-0.2461-0.40650.0922-0.09890.3608-0.0280.00610.40280.01520.373262.089619.244711.7073
48.318-1.6195-5.50273.74672.27054.04370.20460.85840.0770.0519-0.29870.018-0.1917-1.17480.11550.37090.01230.01060.4087-0.01540.361855.337920.803613.3425
58.6424-0.65443.64075.9336-2.91852.86690.013-0.7890.30250.7857-0.3284-0.14510.83230.48810.26930.601600.03270.6816-0.07780.335857.67817.607733.4858
64.33252.0975.84693.51683.2788.18160.0697-1.3448-0.3590.12960.1428-0.1551-0.2749-0.1898-0.18240.363-0.01180.01410.62370.01920.331454.429213.550327.7935
72.2153-1.14062.22888.8657-0.84833.485-0.32720.2022-0.12110.4456-0.154-1.2912-0.04581.22950.4850.4174-0.0521-0.09340.72970.10480.508568.105414.140829.7439
89.40586.70370.30038.35513.77577.82830.30120.5323-1.09110.0683-0.05270.51380.1026-0.0845-0.11640.4290.0625-0.03790.48960.10820.606956.36166.500423.8408
98.75585.78151.33619.60973.43119.7375-0.35341.2546-0.54240.47620.79170.07320.343-0.3035-0.22130.51690.04740.02760.589-0.02370.34258.09725.980318.9601
109.86165.61295.66723.49984.21628.0273-0.1734-0.1514-0.6096-0.35970.2149-1.02140.30370.750.09470.4428-0.02160.02560.535-0.10460.502168.090614.977719.3416
112.90262.8376-4.17854.9767-4.77976.2267-0.58762.2725-0.207-1.20180.89410.98032.0516-1.24-0.26590.9032-0.2602-0.04011.0014-0.08380.788659.63211.876912.6477
122.41721.72951.54764.20815.70228.0747-0.24080.0610.7206-0.73990.7225-0.181-0.64381.1443-0.50590.4037-0.07990.10040.5754-0.00540.448568.965120.235313.7902
134.4136-1.2116-0.3344.52430.12716.3890.4606-1.0613-0.97241.15390.08720.80561.0443-1.4621-0.49470.5283-0.16590.03020.78640.16080.447629.67488.536530.1087
147.85040.04363.30063.751-1.2237.94750.20630.1521-0.2756-0.23540.01270.35140.2567-0.4977-0.15770.3673-0.0113-0.00530.3786-0.020.352229.735413.133210.6333
158.4882-1.01815.47393.5149-1.92234.00630.18090.8594-0.07930.0312-0.21290.00630.2471.1618-0.02930.36490.0156-0.00010.3840.0170.352339.612911.594813.3364
163.33010.5147-1.624.8003-0.49926.0114-0.0119-0.7362-0.05170.51840.15980.0474-0.0998-0.3917-0.04830.4153-0.0128-0.02310.6050.03510.316738.859316.746730.741
172.1688-1.4644-1.93788.04040.57472.0577-0.39150.12980.05230.5706-0.10241.21260.0879-0.96010.58120.4366-0.05630.12740.7579-0.10650.514226.864518.256329.747
188.92417.6045-0.85289.3788-3.22279.4757-0.2480.6380.8264-0.13860.376-0.1711-0.31240.1702-0.06530.44170.06270.01190.4967-0.01890.500237.773726.144921.5181
195.24645.4174-5.11215.708-5.13285.087-0.21740.13810.6177-0.68890.3641.1286-0.0367-0.77-0.02950.4414-0.0356-0.0130.59550.11390.508826.866617.423519.3475
204.65985.2072.36325.92272.61752.4849-1.04291.1567-0.288-1.8070.5962-1.2131-1.39751.79170.60270.7915-0.27940.02381.10230.09790.83735.320330.521312.6424
218.52971.9672-1.72353.2375-5.33389.2647-0.1232-0.0237-0.5501-0.90090.43430.41280.6039-1.0075-0.26330.3704-0.0778-0.09820.58460.01640.381725.991212.16313.7974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 9 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 22 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 37 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 38 through 57 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 58 through 67 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 68 through 77 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 78 through 87 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 88 through 97 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 98 through 107 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 108 through 117 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 118 through 127 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 128 through 134 )A0
13X-RAY DIFFRACTION13chain 'B' and (resid -1 through 9 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 10 through 37 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 38 through 57 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 58 through 77 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 78 through 87 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 88 through 107 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 108 through 117 )B0
20X-RAY DIFFRACTION20chain 'B' and (resid 118 through 127 )B0
21X-RAY DIFFRACTION21chain 'B' and (resid 128 through 134 )B0

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