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- PDB-2z55: Bacterioruberin in the trimeric structure of archaerhodopsin-2 -

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Basic information

Entry
Database: PDB / ID: 2z55
TitleBacterioruberin in the trimeric structure of archaerhodopsin-2
ComponentsArchaerhodopsin-2
KeywordsTRANSPORT PROTEIN / retinal protein / bacterioruberin
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / proton transmembrane transport / plasma membrane
Similarity search - Function
Bacterial rhodopsins retinal binding site. / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BACTERIORUBERIN / 2,3-DI-PHYTANYL-GLYCEROL / RETINAL / Archaerhodopsin-2
Similarity search - Component
Biological speciesHalobacterium sp. AUS-2 (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKouyama, T. / Yoshimura, K.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural role of bacterioruberin in the trimeric structure of archaerhodopsin-2
Authors: Yoshimura, K. / Kouyama, T.
History
DepositionJun 28, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Archaerhodopsin-2
B: Archaerhodopsin-2
D: Archaerhodopsin-2
E: Archaerhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,98420
Polymers109,2514
Non-polymers8,73316
Water1,820101
1
A: Archaerhodopsin-2
hetero molecules

A: Archaerhodopsin-2
hetero molecules

A: Archaerhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,48815
Polymers81,9383
Non-polymers6,55012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area20960 Å2
ΔGint-101 kcal/mol
Surface area24700 Å2
MethodPISA, PQS
2
B: Archaerhodopsin-2
hetero molecules

B: Archaerhodopsin-2
hetero molecules

B: Archaerhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,48815
Polymers81,9383
Non-polymers6,55012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area21080 Å2
ΔGint-87 kcal/mol
Surface area24040 Å2
MethodPISA, PQS
3
D: Archaerhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0006
Polymers27,3131
Non-polymers2,6885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: Archaerhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9914
Polymers27,3131
Non-polymers1,6793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Archaerhodopsin-2
hetero molecules

D: Archaerhodopsin-2
hetero molecules

D: Archaerhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,00118
Polymers81,9383
Non-polymers8,06315
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
MethodPQS
6
E: Archaerhodopsin-2
hetero molecules

E: Archaerhodopsin-2
hetero molecules

E: Archaerhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,97412
Polymers81,9383
Non-polymers5,0369
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
MethodPQS
Unit cell
Length a, b, c (Å)108.830, 108.830, 220.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein / Sugars , 2 types, 8 molecules ABDE

#1: Protein
Archaerhodopsin-2 / AR 2


Mass: 27312.756 Da / Num. of mol.: 4 / Fragment: archaerhodopsin-2 / Source method: isolated from a natural source / Source: (natural) Halobacterium sp. AUS-2 (Halophile) / Strain: aus-2 / References: UniProt: P29563
#2: Polysaccharide
beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-6DManpa1-2DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-2-3/a2-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(2+1)][a-D-Manp]{[(6+1)][b-D-Galp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 113 molecules

#3: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H28O
#4: Chemical
ChemComp-22B / BACTERIORUBERIN


Mass: 741.136 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C50H76O4
#5: Chemical
ChemComp-L2P / 2,3-DI-PHYTANYL-GLYCEROL / 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL


Mass: 653.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C43H88O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.45 Å3/Da / Density % sol: 64.38 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.9M ammonium sulfate, 3.25mg/ml nonyl glucoside, 0.16M NaCl, 8% trehalose, 0.04% Na-azide, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 4, 2006 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→54 Å / Num. all: 51050 / Num. obs: 51050 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.081 / Net I/σ(I): 22.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 5.1 / Num. unique all: 7441 / Rsym value: 0.42 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EI4

2ei4


Resolution: 2.5→15 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: hemihedrally twinned
RfactorNum. reflection% reflectionSelection details
Rfree0.232 4865 -random
Rwork0.201 ---
obs0.201 47521 93.6 %-
all-50784 --
Displacement parametersBiso mean: 42.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.158 Å2-1.073 Å20 Å2
2---0.158 Å20 Å2
3---0.316 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.05 Å-0.09 Å
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7374 0 612 101 8087
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00797
X-RAY DIFFRACTIONc_angle_deg1.322
X-RAY DIFFRACTIONc_dihedral_angle_d17.74
X-RAY DIFFRACTIONc_improper_angle_d0.582

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