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- PDB-3ohw: X-Ray Structure of Phycobilisome LCM core-membrane linker polypep... -

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Basic information

Entry
Database: PDB / ID: 3ohw
TitleX-Ray Structure of Phycobilisome LCM core-membrane linker polypeptide (fragment 721-860) from Synechocystis sp. PCC 6803, Northeast Structural Genomics Consortium Target SgR209E
ComponentsPhycobilisome LCM core-membrane linker polypeptide
KeywordsPROTEIN BINDING / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Lyases / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / lyase activity
Similarity search - Function
Phycobilisome linker domain / serine acetyltransferase, domain 1 / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily ...Phycobilisome linker domain / serine acetyltransferase, domain 1 / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phycobiliprotein ApcE
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsKuzin, A. / Su, M. / Lew, S. / Vorobiev, S.M. / Patel, P. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. ...Kuzin, A. / Su, M. / Lew, S. / Vorobiev, S.M. / Patel, P. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target SgR209E
Authors: Kuzin, A. / Su, M. / Lew, S. / Vorobiev, S.M. / Patel, P. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionAug 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Phycobilisome LCM core-membrane linker polypeptide
A: Phycobilisome LCM core-membrane linker polypeptide


Theoretical massNumber of molelcules
Total (without water)34,6222
Polymers34,6222
Non-polymers00
Water0
1
B: Phycobilisome LCM core-membrane linker polypeptide


Theoretical massNumber of molelcules
Total (without water)17,3111
Polymers17,3111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Phycobilisome LCM core-membrane linker polypeptide


Theoretical massNumber of molelcules
Total (without water)17,3111
Polymers17,3111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.891, 74.881, 66.388
Angle α, β, γ (deg.)90.000, 91.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phycobilisome LCM core-membrane linker polypeptide


Mass: 17311.059 Da / Num. of mol.: 2 / Fragment: sequence database residues 711-858
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: apcE, slr0335 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q55544

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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: 2.15 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 297 K / Method: macrobatch under oik / pH: 7
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution:tryptone 1% (w/v), HEPES sodium 0.05M, PEG3350 20% (w/v), macrobatch under oik, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Aug 10, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 15697 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 26.93 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 10.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→27.753 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.816 / SU ML: 0.39 / σ(F): 5.81 / Phase error: 25.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.266 794 10.01 %
Rwork0.237 --
obs0.24 7930 97.84 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 17.948 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 186.68 Å2 / Biso mean: 27.447 Å2 / Biso min: 2.05 Å2
Baniso -1Baniso -2Baniso -3
1-2.979 Å20 Å2-4.219 Å2
2---1.297 Å20 Å2
3----1.682 Å2
Refinement stepCycle: LAST / Resolution: 2.7→27.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 0 0 2056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082098
X-RAY DIFFRACTIONf_angle_d1.3462828
X-RAY DIFFRACTIONf_chiral_restr0.095302
X-RAY DIFFRACTIONf_plane_restr0.008372
X-RAY DIFFRACTIONf_dihedral_angle_d17.441800
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.701-2.8690.3551240.3041114123893
2.869-3.0910.3161310.281173130497
3.091-3.4010.2821290.2641196132599
3.401-3.8920.2641330.2371213134699
3.892-4.90.2351380.1951207134599
4.9-27.7540.2251390.21612331372100
Refinement TLS params.Method: refined / Origin x: 13.6927 Å / Origin y: 1.4943 Å / Origin z: 17.0359 Å
111213212223313233
T0.0373 Å20.0199 Å2-0.0037 Å2-0.0162 Å20.0003 Å2--0.0259 Å2
L0.0002 °2-0.0113 °2-0.0107 °2--0.0158 °20.0088 °2--0.232 °2
S-0.0456 Å °-0.0056 Å °-0.0038 Å °-0.003 Å °-0.0206 Å °0.0384 Å °0.0037 Å °-0.027 Å °0.026 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB731 - 857
2X-RAY DIFFRACTION1allA731 - 857

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