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- PDB-1dze: Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K -

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Basic information

Entry
Database: PDB / ID: 1dze
TitleStructure of the M Intermediate of Bacteriorhodopsin trapped at 100K
ComponentsBACTERIORHODOPSIN (M INTERMEDIATE)
KeywordsBACTERIORHODOPSIN / PROTON PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / PHOTORECEPTOR / REACTION INTERMEDIATE / HALOBACTERIA / ION PUMP / HELIX / SLIDING
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 / Chem-L4P / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHALOBACTERIUM SALINARIUM (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTakeda, K. / Matsui, Y. / Sato, H. / Hino, T. / Kanamori, E. / Okumura, H. / Yamane, T. / Iizuka, T. / Kamiya, N. / Adachi, S. / Kouyama, T.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of the M Intermediate of Bacteriorhodopsin: Allosteric Structural Changes Mediated by Sliding Movement of a Transmembrane Helix
Authors: Takeda, K. / Matsui, Y. / Kamiya, N. / Adachi, S. / Okumura, H. / Kouyama, T.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Specific Lipid-Protein Interactions in a Novel Honeycomb Lattice Structure of Bacteriorhodopsin
Authors: Sato, H. / Takeda, K. / Tani, K. / Hino, T. / Okada, T. / Nakasako, M. / Kamiya, N. / Kouyama, T.
History
DepositionFeb 25, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
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 / 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 / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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 2.1Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BACTERIORHODOPSIN (M INTERMEDIATE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3358
Polymers26,8141
Non-polymers4,5217
Water32418
1
A: BACTERIORHODOPSIN (M INTERMEDIATE)
hetero molecules

A: BACTERIORHODOPSIN (M INTERMEDIATE)
hetero molecules

A: BACTERIORHODOPSIN (M INTERMEDIATE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,00524
Polymers80,4433
Non-polymers13,56221
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area10290 Å2
ΔGint-79.2 kcal/mol
Surface area31220 Å2
MethodPQS
Unit cell
Length a, b, c (Å)102.400, 102.400, 112.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein BACTERIORHODOPSIN (M INTERMEDIATE)


Mass: 26814.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HALOBACTERIUM SALINARIUM / Source: (natural) HALOBACTERIUM SALINARIUM (Halophile) / Cellular location: CELL MEMBRANE / Strain: JW3 / References: UniProt: P02945
#2: Polysaccharide beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
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 , 6 types, 24 molecules

#3: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#4: 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.: 1 / Source method: obtained synthetically / Formula: C43H89O6P
#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.: 2 / Source method: obtained synthetically / Formula: C43H88O3
#6: 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
#7: Chemical ChemComp-L4P / 3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL / 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL


Mass: 807.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H95O8P
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.17 Å3/Da / Density % sol: 61.19 %
Description: DATA WERE COLLECTED USING THE OSCILLATION METHOD
Crystal growMethod: vapor diffusion / pH: 5.2
Details: THE CRYSTALLIZATION CONSISTS OF TWO STEPS. FIRST, A MIXTURE OF 5 MG/ML PURPLE MEMBRANE, 0.25% OTG, 1 M AMMONIUM SULFATE, 0.16 M NACL, 0.04 M SODIUM CITRATE (PH5.2) , 0.04% NAN3 WAS INCUBATED ...Details: THE CRYSTALLIZATION CONSISTS OF TWO STEPS. FIRST, A MIXTURE OF 5 MG/ML PURPLE MEMBRANE, 0.25% OTG, 1 M AMMONIUM SULFATE, 0.16 M NACL, 0.04 M SODIUM CITRATE (PH5.2) , 0.04% NAN3 WAS INCUBATED AND 15% TREHALOSE AT 305K FOR 5 DAYS. THIS RESULTED IN THE FORMATION OF SPHERICAL VESICLES WITH A DIAMETER OF 50 NM. AFTER SEDIMENTAL MATERIALS WERE REMOVED BY CENTRIFUGATION (4000G X 10 MIN), A SUSPENSION OF THE SPHERICAL VESICLES WAS COOLED TO 278K AND CONCENTRATED BY VAPOR DIFFUSION AGAINST A RESERVOIR SOLUTION CONTAINING 2.0 M AMMONIUM SULFATE 0.08M SODIUM CITRATE (PH 5.2) AND 30% TREHALOSE. INCUBATION FOR A COUPLE OF MONTHS YIELDED HEXAGONAL CRYSTALS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 18, 1998 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 11480 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Rsym value: 0.069
Reflection shellResolution: 2.5→2.59 Å / Rsym value: 0.304 / % possible all: 55.2

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QM8

1qm8


Resolution: 2.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE C-TERMINAL RESIDUES WERE NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 561 5 %RANDOM
Rwork0.257 ---
obs0.257 11017 90.8 %-
Displacement parametersBiso mean: 36 Å2
Baniso -1Baniso -2Baniso -3
1--19.7 Å2-9.8 Å20 Å2
2---19.7 Å20 Å2
3---13.4 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1739 0 247 18 2004
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.22
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.22
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.437 41 5 %
Rwork0.371 756 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2RET_CIS.PARRET_CIS.TOP
X-RAY DIFFRACTION3DPG.PARDPG.TOP
X-RAY DIFFRACTION4GLC.PARGLC.TOP

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