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- PDB-3vhz: Crystal structure of the trans isomer of the L93A mutant of bacte... -

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Basic information

Entry
Database: PDB / ID: 3vhz
TitleCrystal structure of the trans isomer of the L93A mutant of bacteriorhodopsin
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / seven transmembrane helices / cell membrane / retinal protein / light-driven proton pump
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 / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKouyama, T. / Zhang, J.
CitationJournal: Proteins / Year: 2012
Title: Crystal structure of the O intermediate of the Leu93Ala mutant of bacteriorhodopsin
Authors: Zhang, J. / Yamazaki, Y. / Hikake, M. / Murakami, M. / Ihara, K. / Kouyama, T.
History
DepositionSep 13, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / 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.mon_nstd_flag / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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

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Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0595
Polymers28,2281
Non-polymers1,8314
Water77543
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,17615
Polymers84,6843
Non-polymers5,49212
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 area17040 Å2
ΔGint-35 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.600, 102.600, 112.340
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 , 1 types, 1 molecules A

#1: Protein Bacteriorhodopsin / / BR / Bacterioopsin / BO


Mass: 28228.006 Da / Num. of mol.: 1 / Mutation: L93A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium (Halophile) / Strain: ATCC 700922 / JCM 11081 / NRC-1 / Gene: bop, VNG_1467G / Plasmid: pUC18 / Production host: halobacterium (Halophile) / Strain (production host): MPK409 / 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
#4: 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 , 3 types, 45 molecules

#3: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#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.: 43 / 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: 3.02 Å3/Da / Density % sol: 59.32 %
Crystal growTemperature: 283 K / Method: membrane fusion method / pH: 5.2
Details: membrane fusion method, 2.3M ammonium sulfate, 0.05M Na-citrate, pH 5.2, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2011 / Details: Si (111) double crystal monochromator
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→88.9 Å / Num. all: 16031 / Num. obs: 15435 / % possible obs: 96.7 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3 / Redundancy: 8.8 % / Biso Wilson estimate: 47.2 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.068 / Net I/σ(I): 47.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 14.1 / Rsym value: 0.287 / % possible all: 95.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1iw6

1iw6


Resolution: 2.3→15 Å / Occupancy min: 0.87 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2845 916 5.7 %RANDOM
obs0.2524 15397 96 %-
all-16031 --
Solvent computationBsol: 95.7072 Å2
Displacement parametersBiso max: 109.13 Å2 / Biso mean: 47.2861 Å2 / Biso min: 26.18 Å2
Baniso -1Baniso -2Baniso -3
1--11.752 Å2-13.375 Å20 Å2
2---11.752 Å20 Å2
3---23.505 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 123 43 1928
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007514
X-RAY DIFFRACTIONc_angle_deg1.20852
X-RAY DIFFRACTIONc_dihedral_angle_d18.2512
X-RAY DIFFRACTIONc_improper_angle_d0.78653
X-RAY DIFFRACTIONc_mcbond_it1.0421.5
X-RAY DIFFRACTIONc_scbond_it1.5422
X-RAY DIFFRACTIONc_mcangle_it1.7062
X-RAY DIFFRACTIONc_scangle_it2.252.5
LS refinement shellResolution: 2.3→2.34 Å
RfactorNum. reflection
Rfree0.3876 820
Rwork0.3312 -
obs-1397
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4tra.param

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