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- PDB-4hwl: Crystal Structure Analysis of the Bacteriorhodopsin in Facial Amp... -

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Basic information

Entry
Database: PDB / ID: 4hwl
TitleCrystal Structure Analysis of the Bacteriorhodopsin in Facial Amphiphile-7 DMPC Bicelle
ComponentsBacteriorhodopsin
KeywordsPROTON TRANSPORT / Facial Amphiphile-7 DMPC Bicelle / Alpha helical 7 Transmembrane Protein / Photoreceptor / Proton Pump / Retinal Binding / Transmembrane
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
HEXANE / HEPTANE / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLee, S. / Stout, C.D. / Zhang, Q.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Steroid-based facial amphiphiles for stabilization and crystallization of membrane proteins.
Authors: Lee, S.C. / Bennett, B.C. / Hong, W.X. / Fu, Y. / Baker, K.A. / Marcoux, J. / Robinson, C.V. / Ward, A.B. / Halpert, J.R. / Stevens, R.C. / Stout, C.D. / Yeager, M.J. / Zhang, Q.
History
DepositionNov 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...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 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

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Assembly

Deposited unit
A: Bacteriorhodopsin
B: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,84612
Polymers56,5402
Non-polymers1,30610
Water57632
1
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0277
Polymers28,2701
Non-polymers7576
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8195
Polymers28,2701
Non-polymers5494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Bacteriorhodopsin
hetero molecules

B: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,84612
Polymers56,5402
Non-polymers1,30610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area5490 Å2
ΔGint-21 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.160, 113.290, 56.190
Angle α, β, γ (deg.)90.00, 114.27, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 5 - 231 / Label seq-ID: 18 - 244

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 28270.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / Strain: S9 / References: UniProt: P02945

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Non-polymers , 5 types, 42 molecules

#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14
#4: Chemical ChemComp-HP6 / HEPTANE / Heptane


Mass: 100.202 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H16
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 300.15 K / Method: vapor diffusion, sitting drop / pH: 3.4
Details: 3.6M Sodium Phosphate (pH 3.4), 3.5% Triethyleneglycol, 180mM Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 300.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2011
RadiationMonochromator: Slide scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2→46.67 Å / Num. all: 35395 / Num. obs: 34192 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 6.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.7 / Num. unique all: 5132 / % possible all: 95.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASESphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KME

1kme


Resolution: 2→42.08 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.12 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17183 1667 4.8 %RANDOM
Rwork0.15875 ---
all0.15942 35395 --
obs0.15942 33257 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.373 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3512 0 91 32 3635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.023691
X-RAY DIFFRACTIONr_bond_other_d0.0070.023724
X-RAY DIFFRACTIONr_angle_refined_deg1.8791.995018
X-RAY DIFFRACTIONr_angle_other_deg1.31738505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8775452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69322.069116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4915568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5041514
X-RAY DIFFRACTIONr_chiral_restr0.1510.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213998
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02852
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14311 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.143 108 -
Rwork0.117 2382 -
obs-2382 96.62 %

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