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- PDB-4tq2: Structure of S-type Phycobiliprotein Lyase CPES from Guillardia theta -

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Basic information

Entry
Database: PDB / ID: 4tq2
TitleStructure of S-type Phycobiliprotein Lyase CPES from Guillardia theta
ComponentsPutative phycoerythrin lyase
KeywordsLYASE / beta barrel / phycoerythrobilin
Function / homology
Function and homology information


Chromophore lyase CpcS/CpeS / CpeS-like protein / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
HEXANE-1,6-DIOL / Putative phycoerythrin lyase
Similarity search - Component
Biological speciesGuillardia theta CCMP2712 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsGasper, R. / Overkamp, K.E. / Frankenberg-Dinkel, N. / Hofmann, E.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationFR1687/6-1 Germany
Studienstiftung des Deutschen Volkes Germany
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Insights into the Biosynthesis and Assembly of Cryptophycean Phycobiliproteins.
Authors: Overkamp, K.E. / Gasper, R. / Kock, K. / Herrmann, C. / Hofmann, E. / Frankenberg-Dinkel, N.
History
DepositionJun 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Derived calculations / Refinement description
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / software / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_audit_support.funding_organization
Revision 2.1Oct 18, 2017Group: Data collection / Category: diffrn / diffrn_radiation / diffrn_source
Revision 2.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative phycoerythrin lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7782
Polymers21,6601
Non-polymers1181
Water50428
1
A: Putative phycoerythrin lyase
hetero molecules

A: Putative phycoerythrin lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5574
Polymers43,3202
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
Buried area2880 Å2
ΔGint-1 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.830, 116.580, 58.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
SymmetryPoint symmetry: (Schoenflies symbol: D2 (2x2 fold dihedral))
Components on special symmetry positions
IDModelComponents
11A-327-

HOH

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Components

#1: Protein Putative phycoerythrin lyase


Mass: 21660.182 Da / Num. of mol.: 1 / Fragment: Residues 80-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Guillardia theta CCMP2712 (eukaryote) / Gene: GUITHDRAFT_191403 / Plasmid: pASK-IBA7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L1JFC7
#2: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.19 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.6
Details: 0.015M CoCl2, 0.085M sodium acetate pH 4.6, 0.85M 1,6-hexanediol, 7% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97794, 0.97856
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2013
RadiationMonochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.977941
20.978561
ReflectionNumber: 129810 / Rmerge(I) obs: 0.132 / Χ2: 1.14 / D res high: 2.5 Å / Num. obs: 18581 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
11.1819.57417410.039
7.9111.1837910.041
6.467.9149810.064
5.596.4658710.077
55.5965810.067
4.56573410.061
4.234.5678410.067
3.954.2385010.082
3.733.9592110.106
3.543.7395210.124
3.373.54102610.148
3.233.37105710.219
3.13.23109410.271
2.993.1113610.357
2.892.99120510.506
2.82.89118610.617
2.712.8130210.76
2.642.71127510.947
2.562.64136111.184
2.52.56140211.564
ReflectionResolution: 1.95→19.574 Å / Num. obs: 20588 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 13 % / Biso Wilson estimate: 52.8 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.052 / Χ2: 1.005 / Net I/σ(I): 24.26 / Num. measured all: 266849
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.95-20.5932.0941.4220319150214962.17699.6
2-2.060.6841.5981.9219318145114461.66199.7
2.06-2.120.8071.2662.4518309143914341.31999.7
2.12-2.180.890.8523.5417536139113900.88899.9
2.18-2.250.9390.6564.8618199135413540.682100
2.25-2.330.9660.4676.7518025130413010.48599.8
2.33-2.420.9810.3478.6817162124712470.36100
2.42-2.520.9890.24611.7616486121212120.255100
2.52-2.630.9950.16915.9615893119211920.176100
2.63-2.760.9960.12320.7813685109510950.128100
2.76-2.910.9980.09126.5213811105610560.095100
2.91-3.080.9990.06836.1413942101510150.07100
3.08-3.30.9990.04847.66125949489480.05100
3.3-3.5610.03956.19115089049030.04199.9
3.56-3.90.9990.03460.8793598158140.03699.9
3.9-4.360.9990.03268.2684747487460.03399.7
4.36-5.040.9990.02876.5183256716700.0399.9
5.04-6.1710.02972.1565065705700.03100
6.17-8.7210.02768.9546444524510.02999.8
8.72-19.57410.02677.8227542762480.02789.9

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Phasing

PhasingMethod: SAD
Phasing MADD res high: -0 Å / D res low: 0 Å / FOM : 0 / Reflection: 0

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RESOLVEphasing
PDB_EXTRACT3.14data extraction
PHASESphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→19.574 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 1029 5 %
Rwork0.2093 19551 -
obs0.2111 20580 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 253.41 Å2 / Biso mean: 73.4298 Å2 / Biso min: 32.81 Å2
Refinement stepCycle: final / Resolution: 1.95→19.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 22 28 1472
Biso mean--83.09 59.44 -
Num. residues----177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161466
X-RAY DIFFRACTIONf_angle_d1.5441971
X-RAY DIFFRACTIONf_chiral_restr0.067214
X-RAY DIFFRACTIONf_plane_restr0.007253
X-RAY DIFFRACTIONf_dihedral_angle_d18.668550
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.95-2.05270.32861440.314527372881
2.0527-2.18120.34011440.283927542898
2.1812-2.34930.33021460.263727652911
2.3493-2.58530.29491460.247627662912
2.5853-2.95830.28421470.237528002947
2.9583-3.72290.2251480.213428092957
3.7229-19.5750.22271540.18129203074

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