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- PDB-3nph: Crystal structure of the pfam00427 domain from Synechocystis sp. ... -

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Basic information

Entry
Database: PDB / ID: 3nph
TitleCrystal structure of the pfam00427 domain from Synechocystis sp. PCC 6803
ComponentsPhycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2
KeywordsPHOTOSYNTHESIS / pfam00427 domain / Linker protein / phycobiliprotein
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycobilisome linker domain / serine acetyltransferase, domain 1 / Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. ...Phycobilisome linker domain / serine acetyltransferase, domain 1 / Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.849 Å
AuthorsGao, X. / Chen, L. / Wu, J.-W. / Zhang, Y.-Z.
CitationJournal: Mol.Microbiol. / Year: 2011
Title: Crystal structure of the N-terminal domain of linker L(R) and the assembly of cyanobacterial phycobilisome rods
Authors: Gao, X. / Zhang, N. / Wei, T.-D. / Su, H.-N. / Xie, B.-B. / Dong, C.-C. / Zhang, X.-Y. / Chen, X.-L. / Zhou, B.-C. / Wang, Z.-X. / Wu, J.-W. / Zhang, Y.-Z.
History
DepositionJun 28, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 19, 2011Group: Database references
Revision 1.3Dec 14, 2011Group: Database references
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2


Theoretical massNumber of molelcules
Total (without water)17,4581
Polymers17,4581
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.675, 55.675, 79.187
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-185-

HOH

21B-208-

HOH

31B-231-

HOH

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Components

#1: Protein Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2


Mass: 17458.365 Da / Num. of mol.: 1 / Fragment: pfam00427 domain, PBS-linker, UNP residues 19-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DH3) / References: UniProt: P73204
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 1.78 Å3/Da / Density % sol: 31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 3000, 0.1M Bis-Tris buffer (pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.498 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.498 Å / Relative weight: 1
ReflectionResolution: 1.849→39.43 Å / Num. obs: 11164 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.03 Å2
Reflection shellResolution: 1.849→1.91 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.849→22.772 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8205 / SU ML: 0.28 / σ(F): 1.4 / Phase error: 23.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 1117 10.01 %RANDOM
Rwork0.2025 10047 --
obs0.204 11164 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.699 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 83.49 Å2 / Biso mean: 25.7342 Å2 / Biso min: 13.87 Å2
Baniso -1Baniso -2Baniso -3
1--5.8544 Å2-0 Å20 Å2
2---5.8544 Å2-0 Å2
3---2.4044 Å2
Refinement stepCycle: LAST / Resolution: 1.849→22.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 0 141 1232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061116
X-RAY DIFFRACTIONf_angle_d0.9881510
X-RAY DIFFRACTIONf_dihedral_angle_d18.479402
X-RAY DIFFRACTIONf_chiral_restr0.073158
X-RAY DIFFRACTIONf_plane_restr0.004200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8487-1.93280.2721360.21991218X-RAY DIFFRACTION99
1.9328-2.03470.31421350.21261221X-RAY DIFFRACTION100
2.0347-2.16210.28941360.21221229X-RAY DIFFRACTION100
2.1621-2.32880.26511390.21291246X-RAY DIFFRACTION100
2.3288-2.56290.24151380.22111237X-RAY DIFFRACTION100
2.5629-2.93310.3091400.2261262X-RAY DIFFRACTION100
2.9331-3.69290.25511410.20361273X-RAY DIFFRACTION100
3.6929-22.77410.24621520.2091361X-RAY DIFFRACTION100

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