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- PDB-2zzl: Structure of bacteriorhodopsin's M intermediate at pH 7 -

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Basic information

Entry
Database: PDB / ID: 2zzl
TitleStructure of bacteriorhodopsin's M intermediate at pH 7
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / retinal / protein-lipid complex / reaction intermediate / Cell membrane / Chromophore / Hydrogen ion transport / Ion transport / Membrane / Photoreceptor protein / Pyrrolidone carboxylic acid / Receptor / Retinal protein / Sensory transduction / Transmembrane / Transport
Function / homology
Function and homology information


photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / 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
3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL / 2,3-DI-PHYTANYL-GLYCEROL / Chem-L3P / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsYamamoto, M. / Kouyama, T.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structures of Different Substates of Bacteriorhodopsin's M Intermediate at Various pH Levels.
Authors: Yamamoto, M. / Hayakawa, N. / Murakami, M. / Kouyama, T.
History
DepositionFeb 18, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1859
Polymers28,2701
Non-polymers4,9158
Water72140
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,55627
Polymers84,8103
Non-polymers14,74524
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area3890 Å2
ΔGint-52 kcal/mol
Surface area26970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.21, 102.21, 112.48
Angle α, β, γ (deg.)90, 90, 120
Int Tables number177
Space group name H-MP622

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bacteriorhodopsin / / BR


Mass: 28270.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / Strain: JW3 / References: UniProt: P02945

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 3-O-sulfo-beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 584.501 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalp[3S]b1-6DManpa1-2DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a1122h-1a_1-5][a2112h-1b_1-5_3*OSO/3=O/3=O]/1-2-3/a2-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(2+1)][a-D-Manp]{[(6+1)][b-D-Galp3SO3]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-SOG / octyl 1-thio-beta-D-glucopyranoside / 2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL / 1-S-OCTYL-BETA-D-THIOGLUCOSIDE / octyl 1-thio-beta-D-glucoside / octyl 1-thio-D-glucoside / octyl 1-thio-glucoside / N-Octyl beta-D-thioglucopyranoside


Type: D-saccharide / Mass: 308.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O5S / Comment: detergent*YM

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Non-polymers , 5 types, 46 molecules

#3: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#4: Chemical ChemComp-L3P / 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE


Mass: 885.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H94O11P2
#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.: 1 / Source method: obtained synthetically / Formula: C43H88O3
#6: Chemical ChemComp-L1P / 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL / 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCERO-3-PHOSPHATE


Mass: 733.137 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C43H89O6P
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 293 K / Method: membrane fusion method / pH: 5.2
Details: 2.2M ammonium sulfate, 0.1M sodium citrate, 0.16M potasium chloride, 3M ammonium sulfate, 0.1M HEPES pH 7, liquid propane, Membrane fusion method, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.912 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 2.03→44.2 Å / Num. all: 23074 / Num. obs: 21621 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Biso Wilson estimate: 31.68 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 22.8
Reflection shellResolution: 2.03→2.43 Å / Redundancy: 14 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2355 / Rsym value: 0.521 / % possible all: 71.4

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Processing

Software
NameClassification
MAR345dtbdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1iw9

1iw9


Resolution: 2.03→15 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: THE AUTHOR DIDN'T USE THE DIFFRACTION DATA AT LOW RESOLUTIONS IN THE STRUCTRAL ANALYSIS. BECAUSE THE CRYSTAL CONTAINS NATIVE LIPIDS, THE R-FACTOR TENDS TO BECOME VERY HIGH AT A LOW ...Details: THE AUTHOR DIDN'T USE THE DIFFRACTION DATA AT LOW RESOLUTIONS IN THE STRUCTRAL ANALYSIS. BECAUSE THE CRYSTAL CONTAINS NATIVE LIPIDS, THE R-FACTOR TENDS TO BECOME VERY HIGH AT A LOW RESOLUTION (THAN 15 ANGSTROM). THIS IS PARTLY BECAUSE ALL THE NATIVE LIPIDS THAT MIGHT EXIST IN THE CRYSTAL ARE NOT INCLUDED IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 18197 -RANDOM
Rwork0.207 ---
obs0.207 18197 88.3 %-
all-23984 --
Displacement parametersBiso mean: 41.47 Å2
Baniso -1Baniso -2Baniso -3
1--4.469 Å2-5.345 Å20 Å2
2---4.469 Å20 Å2
3---8.937 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-15 Å
Luzzati sigma a0.13 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2.03→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 322 40 2127
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.17599
X-RAY DIFFRACTIONc_bond_d0.006981
X-RAY DIFFRACTIONc_dihedral_angle_d17.5706
X-RAY DIFFRACTIONc_improper_angle_d0.76763

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