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- PDB-3mwn: Structure of the Novel 14 kDa Fragment of alpha-Subunit of Phycoe... -

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Basic information

Entry
Database: PDB / ID: 3mwn
TitleStructure of the Novel 14 kDa Fragment of alpha-Subunit of Phycoerythrin from the Starving Cyanobacterium Phormidium Tenue
ComponentsPHYCOERYTHRIN
KeywordsELECTRON TRANSPORT / PHYCOERYTHRIN / CYANOBACTERIUM
Function / homology
Function and homology information


: / : / phycobilisome / photosynthesis
Similarity search - Function
Phycocyanins / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHYCOCYANOBILIN / C-phycoerythrin
Similarity search - Component
Biological speciesPHORMIDIUM TENUE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSoni, B.R. / Hasan, M.I. / Parmar, A. / Ethayathulla, A.S. / Kumar, R.P. / Singh, N.K. / Sinha, M. / Kaur, P. / Yadav, S. / Sharma, S. ...Soni, B.R. / Hasan, M.I. / Parmar, A. / Ethayathulla, A.S. / Kumar, R.P. / Singh, N.K. / Sinha, M. / Kaur, P. / Yadav, S. / Sharma, S. / Madamwar, D. / Singh, T.P.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Structure of the novel 14kDa fragment of alpha-subunit of phycoerythrin from the starving cyanobacterium Phormidium tenue.
Authors: Soni, B.R. / Hasan, M.I. / Parmar, A. / Ethayathulla, A.S. / Kumar, R.P. / Singh, N.K. / Sinha, M. / Kaur, P. / Yadav, S. / Sharma, S. / Madamwar, D. / Singh, T.P.
History
DepositionMay 6, 2010Deposition site: RCSB / Processing site: PDBJ
SupersessionJun 30, 2010ID: 2G9M
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 7, 2011Group: Database references
Revision 1.3Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHYCOERYTHRIN
B: PHYCOERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6466
Polymers29,2912
Non-polymers2,3554
Water97354
1
A: PHYCOERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8233
Polymers14,6451
Non-polymers1,1772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHYCOERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8233
Polymers14,6451
Non-polymers1,1772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.357, 83.789, 62.484
Angle α, β, γ (deg.)90.00, 90.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHYCOERYTHRIN /


Mass: 14645.446 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) PHORMIDIUM TENUE (bacteria) / References: UniProt: A4L2N4*PLUS
#2: Chemical
ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H40N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 5.12 Å3/Da / Density % sol: 72.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50MM SODIUM CACODYLATE, 20% PEG 2000, 30MM AMMONIUM SULFATE, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 / Wavelength: 1.5414 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 6, 2005 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.54141
Reflection twinOperator: h,-k,-l / Fraction: 0.4
ReflectionResolution: 2.6→20 Å / Num. all: 18133 / Num. obs: 18133 / % possible obs: 85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 36 Å2 / Rsym value: 0.136 / Net I/σ(I): 5
Reflection shellResolution: 2.6→2.69 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.55 / % possible all: 92.1

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Processing

Software
NameClassification
MAR345dtbdata collection
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LIA

1lia


Resolution: 2.6→10 Å / Num. parameters: 8896 / Num. restraintsaints: 9060 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: THIS IS A TWINNED STRUCTURE. THE TWINNING OPERATOR IS (H, -K, -L) AND THE TWINNING FRACTION IS 0.4. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.286 640 4.2 %RANDOM
Rwork0.238 ---
all0.258 18133 --
obs0.238 15225 84.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 33.5 Å2
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 0
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 172 54 2242
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.025
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.015
X-RAY DIFFRACTIONs_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.103
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.196
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.085
X-RAY DIFFRACTIONs_approx_iso_adps0

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