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- PDB-4o4s: Crystal structure of phycobiliprotein lyase CpcT complexed with p... -

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Basic information

Entry
Database: PDB / ID: 4o4s
TitleCrystal structure of phycobiliprotein lyase CpcT complexed with phycocyanobilin (PCB)
ComponentsPhycocyanobilin lyase CpcT
KeywordsLYASE / beta-barrel / phycocyanobilin / BILIN LYASE
Function / homology
Function and homology information


protein-phycocyanobilin linkage / Lyases / lyase activity
Similarity search - Function
CpcT/CpeT domain / Chromophore lyase CpcT/CpeT / Chromophore lyase CpcT/CpeT superfamily / CpeT/CpcT family (DUF1001) / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHYCOCYANOBILIN / Phycocyanobilin lyase CpcT
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhou, W. / Ding, W.-L. / Zeng, X.-l. / Dong, L.-L. / Zhao, B. / Zhou, M. / Scheer, H. / Zhao, K.-H. / Yang, X.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure and Mechanism of the Phycobiliprotein Lyase CpcT.
Authors: Zhou, W. / Ding, W.L. / Zeng, X.L. / Dong, L.L. / Zhao, B. / Zhou, M. / Scheer, H. / Zhao, K.H. / Yang, X.
History
DepositionDec 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Oct 15, 2014Group: Database references
Revision 1.3Sep 20, 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_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Jan 10, 2024Group: Derived calculations / Category: struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phycocyanobilin lyase CpcT
B: Phycocyanobilin lyase CpcT
I: Phycocyanobilin lyase CpcT
J: Phycocyanobilin lyase CpcT
C: Phycocyanobilin lyase CpcT
D: Phycocyanobilin lyase CpcT
E: Phycocyanobilin lyase CpcT
F: Phycocyanobilin lyase CpcT
G: Phycocyanobilin lyase CpcT
H: Phycocyanobilin lyase CpcT
K: Phycocyanobilin lyase CpcT
L: Phycocyanobilin lyase CpcT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,04624
Polymers290,98112
Non-polymers7,06412
Water30617
1
A: Phycocyanobilin lyase CpcT
B: Phycocyanobilin lyase CpcT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6744
Polymers48,4972
Non-polymers1,1772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-12 kcal/mol
Surface area18760 Å2
MethodPISA
2
I: Phycocyanobilin lyase CpcT
J: Phycocyanobilin lyase CpcT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6744
Polymers48,4972
Non-polymers1,1772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-13 kcal/mol
Surface area18810 Å2
MethodPISA
3
C: Phycocyanobilin lyase CpcT
D: Phycocyanobilin lyase CpcT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6744
Polymers48,4972
Non-polymers1,1772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-12 kcal/mol
Surface area18670 Å2
MethodPISA
4
E: Phycocyanobilin lyase CpcT
F: Phycocyanobilin lyase CpcT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6744
Polymers48,4972
Non-polymers1,1772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-13 kcal/mol
Surface area18830 Å2
MethodPISA
5
G: Phycocyanobilin lyase CpcT
H: Phycocyanobilin lyase CpcT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6744
Polymers48,4972
Non-polymers1,1772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-12 kcal/mol
Surface area18650 Å2
MethodPISA
6
K: Phycocyanobilin lyase CpcT
L: Phycocyanobilin lyase CpcT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6744
Polymers48,4972
Non-polymers1,1772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-13 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.746, 69.601, 162.595
Angle α, β, γ (deg.)90.21, 90.28, 60.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Phycocyanobilin lyase CpcT


Mass: 24248.445 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / UTEX 2576 / Gene: cpcT1, cpeT1, all5339 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YLF9, Lyases
#2: Chemical
ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C33H40N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 47.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MgCl2 6H2O (0.1M), Bis-Tris (0.1 M, pH 5.5) and polyethylene glycol 3350 (14% w/v), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 17, 2013
RadiationMonochromator: diamond laue monochromators / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 92813 / Num. obs: 77314 / % possible obs: 83.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4O4O

4o4o


Resolution: 2.5→29.747 Å / SU ML: 0.43 / σ(F): 1.1 / Phase error: 30.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2485 7427 5.05 %
Rwork0.1802 --
obs0.1836 146956 80.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→29.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19170 0 516 17 19703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0120235
X-RAY DIFFRACTIONf_angle_d1.51627438
X-RAY DIFFRACTIONf_dihedral_angle_d15.8047356
X-RAY DIFFRACTIONf_chiral_restr0.0822829
X-RAY DIFFRACTIONf_plane_restr0.0063543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.52840.38682070.35624441X-RAY DIFFRACTION77
2.5284-2.55810.34262460.32174579X-RAY DIFFRACTION79
2.5581-2.58930.38882590.32254612X-RAY DIFFRACTION79
2.5893-2.62210.36032820.32374594X-RAY DIFFRACTION81
2.6221-2.65660.34992170.31514660X-RAY DIFFRACTION81
2.6566-2.69290.37792510.31774715X-RAY DIFFRACTION79
2.6929-2.73140.35562310.30874674X-RAY DIFFRACTION82
2.7314-2.77210.36562450.30754690X-RAY DIFFRACTION79
2.7721-2.81540.36332350.29414655X-RAY DIFFRACTION80
2.8154-2.86150.33182560.26254608X-RAY DIFFRACTION81
2.8615-2.91080.29732440.2514636X-RAY DIFFRACTION79
2.9108-2.96370.31572730.25444621X-RAY DIFFRACTION81
2.9637-3.02060.35962780.26394666X-RAY DIFFRACTION78
3.0206-3.08220.32962140.23554521X-RAY DIFFRACTION80
3.0822-3.14920.28952400.23214668X-RAY DIFFRACTION79
3.1492-3.22240.28842910.2284583X-RAY DIFFRACTION80
3.2224-3.30290.32222420.21974541X-RAY DIFFRACTION78
3.3029-3.3920.28542540.19584588X-RAY DIFFRACTION80
3.392-3.49170.2992320.20094619X-RAY DIFFRACTION78
3.4917-3.60420.2692170.18924108X-RAY DIFFRACTION72
3.6042-3.73280.26761730.20313184X-RAY DIFFRACTION55
3.7328-3.88190.27072340.18264522X-RAY DIFFRACTION76
3.8819-4.05820.25392050.16944064X-RAY DIFFRACTION71
4.0582-4.27160.20932810.14574687X-RAY DIFFRACTION82
4.2716-4.53830.18352390.12024759X-RAY DIFFRACTION82
4.5383-4.88730.16682410.11344845X-RAY DIFFRACTION83
4.8873-5.37660.19882950.12565410X-RAY DIFFRACTION92
5.3766-6.14860.21212700.13525581X-RAY DIFFRACTION97
6.1486-7.72410.22642890.15025658X-RAY DIFFRACTION96
7.7241-29.74860.1912860.15295040X-RAY DIFFRACTION88
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)
12.6165-2.06040.1551.8147-1.07063.5971-0.1071-0.2988-0.45410.10780.13640.08430.1131-0.0895-0.03840.2642-0.089-0.01480.61410.13080.53229.677526.3024-50.1579
23.6131.2415-0.86583.1265-1.96434.9159-0.07850.82080.4262-0.16020.0969-0.1398-0.4602-0.2049-0.02050.37740.03990.06340.64170.13660.536911.156153.8142-74.3539
30.5774-0.4179-0.92213.30140.51323.2054-0.03430.1271-0.1904-0.39980.0953-0.5162-0.03290.1387-0.04950.4959-0.1910.12860.4061-0.09240.5775-22.83427.4747-110.0157
44.43010.6906-2.05272.51350.28835.23610.314-0.35260.08650.6149-0.34570.3871-0.375-0.35740.03130.5701-0.09850.12490.4093-0.0310.5046-47.469119.8906-85.8034
53.38980.6979-1.11891.02160.37912.95710.139-0.23030.36920.2096-0.12220.3347-0.093-0.0202-0.02880.5489-0.15260.11120.3696-0.07450.5198-16.644744.1343-104.38
62.1369-1.3076-1.43163.21991.134.6713-0.16920.2035-0.218-0.64830.1872-0.32790.26690.4039-0.00490.5779-0.15730.11230.4979-0.12240.55386.282429.3013-128.5408
70.90330.73070.89333.42370.87423.5576-0.0896-0.12040.16670.40670.104-0.4987-0.08120.1622-0.01380.44680.1531-0.12640.3961-0.06010.526811.24658.46454.1258
84.1418-0.4681.82522.50820.5745.43530.30160.2944-0.2165-0.6182-0.3360.55250.3395-0.4341-0.00260.55630.058-0.13770.4215-0.0280.5277-13.099345.9343-20.1961
93.27931.3554-0.30461.9211-0.98113.0695-0.08110.34930.595-0.18710.12290.0868-0.0886-0.1349-0.04160.27340.0061-0.00610.63830.1450.551-25.284339.2182-55.8009
103.2249-1.57980.80313.1453-2.0024.8823-0.126-0.7386-0.4450.11810.1022-0.02390.4397-0.07510.0220.3888-0.0669-0.05740.64080.15920.5339-23.849812.0145-31.6186
113.37-0.8750.99241.11280.2963.4310.1380.2263-0.4418-0.2523-0.08370.35410.1934-0.0018-0.05110.51340.1035-0.11340.3249-0.09880.53417.682321.7503-1.5697
121.8330.82851.50954.32531.86615.0905-0.177-0.16280.26070.70540.2177-0.3989-0.15950.612-0.03280.52480.1036-0.09260.5236-0.12130.498740.381736.643722.6156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J
11X-RAY DIFFRACTION11chain K
12X-RAY DIFFRACTION12chain L

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