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- PDB-1b8d: CRYSTAL STRUCTURE OF A PHYCOUROBILIN-CONTAINING PHYCOERYTHRIN -

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Basic information

Entry
Database: PDB / ID: 1b8d
TitleCRYSTAL STRUCTURE OF A PHYCOUROBILIN-CONTAINING PHYCOERYTHRIN
Components(PROTEIN (RHODOPHYTAN PHYCOERYTHRIN ...) x 3
KeywordsPHOTOSYNTHESIS / LIGHT-HARVESTING COMPLEX / RED ALGAE / PHYCOBILIPROTEIN
Function / homology
Function and homology information


: / : / phycobilisome / chloroplast thylakoid membrane / 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
PHYCOERYTHROBILIN / PHYCOUROBILIN / R-phycoerythrin beta chain / R-phycoerythrin alpha chain
Similarity search - Component
Biological speciesGriffithsia monilis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRitter, S. / Hiller, R.G. / Wrench, P.M. / Welte, W. / Diederichs, K.
CitationJournal: J.Struct.Biol. / Year: 1999
Title: Crystal structure of a phycourobilin-containing phycoerythrin at 1.90-A resolution.
Authors: Ritter, S. / Hiller, R.G. / Wrench, P.M. / Welte, W. / Diederichs, K.
History
DepositionJan 29, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Feb 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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_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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (ALPHA CHAIN))
B: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (BETA CHAIN))
K: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (ALPHA CHAIN))
L: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (BETA CHAIN))
G: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (GAMMA CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,94715
Polymers73,0565
Non-polymers5,89110
Water5,999333
1
A: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (ALPHA CHAIN))
B: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (BETA CHAIN))
K: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (ALPHA CHAIN))
L: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (BETA CHAIN))
G: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (GAMMA CHAIN))
hetero molecules

A: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (ALPHA CHAIN))
B: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (BETA CHAIN))
K: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (ALPHA CHAIN))
L: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (BETA CHAIN))
G: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (GAMMA CHAIN))
hetero molecules

A: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (ALPHA CHAIN))
B: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (BETA CHAIN))
K: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (ALPHA CHAIN))
L: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (BETA CHAIN))
G: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (GAMMA CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,84245
Polymers219,16915
Non-polymers17,67330
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)187.350, 187.350, 59.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.357729, -0.933826, 0.000306), (-0.933819, 0.357725, -0.003899), (0.003531, -0.001681, -0.999992)-0.0209, 0.0245, -0.2378
2given(-0.358491, -0.93352, 0.00494), (-0.933532, 0.358476, -0.003614), (0.001603, -0.005908, -0.999981)0.0247, 0.0075, -0.329

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Components

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PROTEIN (RHODOPHYTAN PHYCOERYTHRIN ... , 3 types, 5 molecules AKBLG

#1: Protein PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (ALPHA CHAIN))


Mass: 17687.834 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THE PHYCOBILISOMES ARE LOCATED ON THE STROMAL SIDE OF THE THYLAKOID MEMBRANES.
Source: (natural) Griffithsia monilis (eukaryote) / Organelle: RHODOPLAST / References: UniProt: O36005
#2: Protein PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (BETA CHAIN))


Mass: 18511.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THE PHYCOBILISOMES ARE LOCATED ON THE STROMAL SIDE OF THE THYLAKOID MEMBRANES.
Source: (natural) Griffithsia monilis (eukaryote) / Organelle: RHODOPLAST / References: UniProt: O36004
#3: Protein/peptide PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (GAMMA CHAIN))


Mass: 656.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Griffithsia monilis (eukaryote) / Organelle: RHODOPLAST

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Non-polymers , 3 types, 343 molecules

#4: Chemical
ChemComp-PEB / PHYCOERYTHROBILIN / Phycoerythrobilin


Mass: 588.694 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C33H40N4O6
#5: Chemical ChemComp-PUB / PHYCOUROBILIN / Phycourobilin


Mass: 590.710 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H42N4O6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 7.5
Details: 700MM SODIUM ACETATE,5MM KCL,100MM IMIDAZOLE, PH 7.5 AT 17C
Crystal grow
*PLUS
Method: other
Details: .refer to Ritter, S., (1997) Protein Peptide Lett., 4, 69.

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.82→15 Å / Num. obs: 67598 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.059
Reflection shellResolution: 1.82→2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.313 / % possible all: 92
Reflection
*PLUS
% possible obs: 96.8 % / Num. measured all: 131195
Reflection shell
*PLUS
% possible obs: 92 % / Num. unique obs: 15857 / Num. measured obs: 28679

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CPC

1cpc


Resolution: 1.9→100 Å / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: INDIVIDUAL B-FAC REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.227 -10 %RANDOM
Rwork0.175 ---
obs-131195 97 %-
Displacement parametersBiso mean: 22.15 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6275 0 460 999 7734
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d17.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.75
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.896
X-RAY DIFFRACTIONx_mcangle_it2.698
X-RAY DIFFRACTIONx_scbond_it3.738
X-RAY DIFFRACTIONx_scangle_it5.210
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Weight Biso : 2 / Weight position: 1

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)
11RESTRAINTS0.4540.4876
220.5180.4857
LS refinement shellResolution: 1.9→1.97 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.2723 -
Rwork0.2418 2807
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARHCSDX.PHYCOASNTOPHCSDX.PHYCOASN
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION4TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg17.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.75

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