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- PDB-1iw9: Crystal Structure of the M Intermediate of Bacteriorhodopsin -

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Basic information

Entry
Database: PDB / ID: 1iw9
TitleCrystal Structure of the M Intermediate of Bacteriorhodopsin
Componentsbacteriorhodopsin
KeywordsPROTON TRANSPORT / 7 Transmembrane Helices / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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
2,3-DI-PHYTANYL-GLYCEROL / Chem-L3P / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTakeda, K. / Matsui, Y. / Kamiya, N. / Adachi, S. / Okumura, H. / Kouyama, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
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: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of the L Intermediate of Bacteriorhodopsin: Evidence for Vertical Translocation of a Water Molecule during the Proton Pumping Cycle
Authors: Kouyama, T. / Nishikawa, T. / Tokuhisa, T. / Okumura, H.
History
DepositionApr 25, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / database_PDB_caveat / 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_unobs_or_zero_occ_residues / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7978
Polymers26,8141
Non-polymers4,9837
Water45025
1
A: bacteriorhodopsin
hetero molecules

A: bacteriorhodopsin
hetero molecules

A: bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,39124
Polymers80,4433
Non-polymers14,94821
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 area28460 Å2
ΔGint-190 kcal/mol
Surface area24010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)102.3, 102.3, 112.3
Angle α, β, γ (deg.)90, 90, 120
Int Tables number177
Space group name H-MP622
DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations:1-y, x-y, z and 1-x+y, 1-x, z

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein bacteriorhodopsin /


Mass: 26814.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / 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 , 4 types, 31 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.: 4 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: ammonium sulfate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 10 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlpurple membrane sheets1drop
22.5 mg/mloctylthioglucoside1drop
31.0 Mammonium sulfate1drop
40.16 M1dropNaCl
512 %(w/v)trehalose1drop
60.04 %(w/v)1dropNaN3
70.08 Msodium citrate1droppH5.2
81.9-2.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.708 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 18, 1998 / Details: mirrors
RadiationMonochromator: DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.708 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 12434 / Num. obs: 11480 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Rmerge(I) obs: 0.069
Reflection shellResolution: 2.5→2.59 Å / Rsym value: 0.304 / % possible all: 55.2
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 10066 / % possible obs: 92.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 92.1 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1dze

1dze


Resolution: 2.5→15.3 Å / Isotropic thermal model: Overall / Cross valid method: troughout / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1085 -random
Rwork0.224 ---
obs0.224 10491 84 %-
all-12488 --
Displacement parametersBiso mean: 47 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å2-3.256 Å20 Å2
2---1.38 Å20 Å2
3---2.761 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-8 Å
Luzzati sigma a0.4 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.5→15.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 298 25 2073
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.194
X-RAY DIFFRACTIONc_dihedral_angle_d18.103
X-RAY DIFFRACTIONc_improper_angle_d0.775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
2.5-2.590.342410.288X-RAY DIFFRACTION3596
2.69-2.810.3371000.273X-RAY DIFFRACTION9516
2.96-3.150.2931240.227X-RAY DIFFRACTION11926
3.39-3.720.291220.21X-RAY DIFFRACTION12236
4.25-5.320.2251290.212X-RAY DIFFRACTION12676
5.32-15.30.2731440.245X-RAY DIFFRACTION13286
Refinement
*PLUS
Lowest resolution: 28 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.231
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.103
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.775

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