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- PDB-4rmp: Crystal structure of allophycocyanin from marine cyanobacterium P... -

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Basic information

Entry
Database: PDB / ID: 4rmp
TitleCrystal structure of allophycocyanin from marine cyanobacterium Phormidium sp. A09DM
Components(Allophycocyanin) x 2
KeywordsPHOTOSYNTHESIS / Phycocyanobilin chromophore / Globin-like fold (SCOP / 46457) / Light harvesting Phycobiliprotein
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Allophycocyanin, beta subunit / 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 / Allophycocyanin / Allophycocyanin
Similarity search - Component
Biological speciesPhormidium rubidum A09DM (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.506 Å
AuthorsKumar, V. / Gupta, G.D. / Sonani, R.R. / Madamwar, D.
CitationJournal: Plos One / Year: 2015
Title: Crystal Structure of Allophycocyanin from Marine Cyanobacterium Phormidium sp. A09DM.
Authors: Sonani, R.R. / Gupta, G.D. / Madamwar, D. / Kumar, V.
History
DepositionOct 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / software / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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_ref_seq_dif.details / _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: Allophycocyanin
B: Allophycocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1094
Polymers34,9322
Non-polymers1,1772
Water3,225179
1
A: Allophycocyanin
B: Allophycocyanin
hetero molecules

A: Allophycocyanin
B: Allophycocyanin
hetero molecules

A: Allophycocyanin
B: Allophycocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,32712
Polymers104,7956
Non-polymers3,5326
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area20570 Å2
ΔGint-211 kcal/mol
Surface area39330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.242, 101.242, 193.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsTHE ASYMMETRIC UNIT CONTAINS ONE EACH A AND B-CHAINS WHICH FORM A HETERODIMER (KNOWN AS ALPHA/BETA MONOMER). THREE ALPHA/BETA MONOMERS FORM A BIOLOGICAL UNIT. THE HEXAMER (TRIMER of ALPHA/BETA MONOMERS) IS GENERATED BY CRYSTALLOGRAPHIC SYMMETRY

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Components

#1: Protein Allophycocyanin


Mass: 17492.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Marine cyanobacterium isolated from rocky shores of Gujarat
Source: (natural) Phormidium rubidum A09DM (bacteria) / References: UniProt: A0A078K1U6
#2: Protein Allophycocyanin


Mass: 17438.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Marine cyanobacterium isolated from rocky shores of Gujarat
Source: (natural) Phormidium rubidum A09DM (bacteria) / References: UniProt: A0A078K4M9
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNATURAL VARIANTS OF THE UNP REFERENCE, AS CONFIRMED BY NUCLEOTIDE SEQUENCING

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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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% (w/v) PEG 6000, 0.1M bicine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 17, 2014 / Details: HELIOS Cu X-RAY OPTICS
RadiationMonochromator: HELIOS Cu X-RAY OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.506→35 Å / Num. all: 13362 / Num. obs: 13362 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.8 % / Biso Wilson estimate: 41.97 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 22.8
Reflection shellResolution: 2.506→2.64 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 5.3 / Num. unique all: 1903 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
autoPROCdata scaling
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KN1

1kn1


Resolution: 2.506→29.226 Å / SU ML: 0.28 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.82 / Stereochemistry target values: ML
Details: The covalent bonds between S atoms of Cys-81 and the chromophore (CYC) were restrained to a distance of 1.8A for both A and B chains
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 680 5.09 %Random
Rwork0.1581 ---
obs0.1617 13362 99.87 %-
all-13362 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.266 Å
Refinement stepCycle: LAST / Resolution: 2.506→29.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2435 0 86 179 2700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082575
X-RAY DIFFRACTIONf_angle_d1.6483495
X-RAY DIFFRACTIONf_dihedral_angle_d16.204950
X-RAY DIFFRACTIONf_chiral_restr0.037393
X-RAY DIFFRACTIONf_plane_restr0.005451
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.506-2.69950.29261420.199624782478
2.6995-2.97090.29851310.200425192519
2.9709-3.40030.30061320.186125132513
3.4003-4.28180.1961310.141125462546
4.2818-29.2280.171440.127626262626

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