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- PDB-4md1: Orange species of bacteriorhodopsin from Halobacterium salinarum -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4md1
TitleOrange species of bacteriorhodopsin from Halobacterium salinarum
ComponentsBacteriorhodopsin
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN / seven transmembrane helix/Bacterial rhodopsins / proton pumping / membrane
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 / Chem-SQL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium sp. NRC-1 (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsBorshchevskiy, V. / Erofeev, I. / Round, E. / Weik, M. / Ishchenko, A. / Gushchin, I. / Mishin, A. / Bueldt, G. / Gordeliy, V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Low-dose X-ray radiation induces structural alterations in proteins.
Authors: Borshchevskiy, V. / Round, E. / Erofeev, I. / Weik, M. / Ishchenko, A. / Gushchin, I. / Mishin, A. / Willbold, D. / Buldt, G. / Gordeliy, V.
History
DepositionAug 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Non-polymer description / Structure summary
Revision 1.2Jan 29, 2020Group: Advisory / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)39,26621
Polymers26,8141
Non-polymers12,45220
Water90150
1
A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules

A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,79963
Polymers80,4433
Non-polymers37,35660
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area22490 Å2
ΔGint-141 kcal/mol
Surface area25600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.910, 60.910, 110.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Bacteriorhodopsin / BR / Bacterioopsin / BO


Mass: 26814.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium sp. NRC-1 (Halophile) / Strain: S9 / References: UniProt: P02945
#2: 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.: 18 / Source method: obtained synthetically / Formula: C43H88O3
#3: Chemical ChemComp-SQL / (6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene / squalene


Mass: 410.718 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H50
#4: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 295 K / Method: in meso / pH: 5.6
Details: Crystals were obtained in a lipidic cubic phase of monoolein, pH 5.6, in meso, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 15, 2009
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.73→23.44 Å / Num. all: 22526 / Num. obs: 22526 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.4
Reflection shellResolution: 1.73→1.82 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3327 / % possible all: 95.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1c3w

1c3w


Resolution: 1.73→23.44 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.19 1160 Random, consistent with ground state data
Rwork0.146 --
all0.148 22519 -
obs0.148 22519 -
Refinement stepCycle: LAST / Resolution: 1.73→23.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 189 50 1976
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d_prot0.012
X-RAY DIFFRACTIONf_angle_d_prot1.6
X-RAY DIFFRACTIONf_dihedral_angle_d_prot11.95
X-RAY DIFFRACTIONf_chiral_restr0.084

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