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- PDB-4wav: Crystal Structure of Haloquadratum walsbyi bacteriorhodopsin muta... -

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Basic information

Entry
Database: PDB / ID: 4wav
TitleCrystal Structure of Haloquadratum walsbyi bacteriorhodopsin mutant D93N
ComponentsBacteriorhodopsin-I
KeywordsTRANSPORT PROTEIN / Bacteriorhodopsin / proton pump / Membrane protein
Function / homology
Function and homology information


: / photoreceptor activity / phototransduction / monoatomic ion channel activity / membrane => GO:0016020 / 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
Chem-MPG / RETINAL / Bacteriorhodopsin-I
Similarity search - Component
Biological speciesHaloquadratum walsbyi C23 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsWang, A.H.J. / Hsu, M.F. / Yang, C.S. / Fu, H.Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science CouncilNSC 102-2319-B-001-003 Taiwan
CitationJournal: To be published
Title: Crystal structure of an acid-tolerant light-driven proton pump at 1.85 Angstroms resolution
Authors: Hsu, M.F. / Fu, H.Y. / Cai, C.J. / Yi, S.P. / Yang, C.S. / Wang, A.H.J.
History
DepositionSep 2, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Advisory / Data collection ...Advisory / 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 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriorhodopsin-I
B: Bacteriorhodopsin-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2926
Polymers57,0102
Non-polymers1,2824
Water2,882160
1
A: Bacteriorhodopsin-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5034
Polymers28,5051
Non-polymers9983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacteriorhodopsin-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7902
Polymers28,5051
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.860, 131.942, 235.423
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Bacteriorhodopsin-I /


Mass: 28505.104 Da / Num. of mol.: 2 / Mutation: D93N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloquadratum walsbyi C23 (archaea) / Gene: bop1, Hqrw_1016 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: G0LFX8
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7 / Details: calcium chloride, HEPES, PEG 400

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A / Type: OTHER / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 3, 2013 / Details: Inter-Frame
RadiationMonochromator: Fixed-Exit Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 11796 / % possible obs: 97.2 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.149 / Χ2: 0.925 / Net I/av σ(I): 12.621 / Net I/σ(I): 5.7 / Num. measured all: 72386
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.856.20.9725990.89298
2.85-2.96.20.8545610.88898.1
2.9-2.966.30.7355870.85893.8
2.96-3.026.30.8225490.89293.7
3.02-3.086.40.6085700.901100
3.08-3.156.10.5715740.89298.6
3.15-3.236.20.4935890.95597
3.23-3.326.30.3985660.95390.7
3.32-3.426.30.3615600.97299.6
3.42-3.536.10.285830.97999.5
3.53-3.656.10.2315770.97394.4
3.65-3.86.40.1745671.00692.5
3.8-3.976.20.1395850.93899.5
3.97-4.1860.1055820.89795.7
4.18-4.446.10.0775830.93896.5
4.44-4.785.90.076061.11499.7
4.78-5.265.90.0676131.04298.6
5.26-6.025.90.0746300.86599.7
6.02-7.566.10.0656390.87399.8
7.56-305.80.0236760.69998.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
Blu-Icedata reduction
MOLREP11.0.05phasing
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VGO
Resolution: 2.8→26.12 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2392 / WRfactor Rwork: 0.1816 / FOM work R set: 0.8414 / SU B: 12.122 / SU ML: 0.247 / SU Rfree: 0.4402 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 504 4.8 %RANDOM
Rwork0.1816 ---
obs0.1844 9924 86.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.17 Å2 / Biso mean: 27.78 Å2 / Biso min: 5.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å20 Å2
2--0.29 Å20 Å2
3----2.35 Å2
Refinement stepCycle: final / Resolution: 2.8→26.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 0 88 160 3742
Biso mean--34.41 22.1 -
Num. residues----453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023667
X-RAY DIFFRACTIONr_bond_other_d0.0020.023663
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9864990
X-RAY DIFFRACTIONr_angle_other_deg0.90938340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4055453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.35422.672131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.14615560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9111518
X-RAY DIFFRACTIONr_chiral_restr0.0850.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024049
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02869
LS refinement shellResolution: 2.802→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 10 -
Rwork0.172 278 -
all-288 -
obs--33.14 %

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