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- PDB-9kme: Crystal structure of soluble bacteriorhodopsin NeuroBR_A -

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Basic information

Entry
Database: PDB / ID: 9kme
TitleCrystal structure of soluble bacteriorhodopsin NeuroBR_A
Componentssoluble bacteriorhodopsin
KeywordsDE NOVO PROTEIN / soluble bacteriorhodopsin
Function / homologyRETINAL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsNikolaev, A. / Remeeva, A. / Kapranov, I. / Borshchevskiy, V. / Gushchin, I.
Funding support Russian Federation, 3items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
Ministry of Science and Higher Education of the Russian Federation075-03-2024-117, project FSMG-2021-0002 Russian Federation
Russian Science Foundation21-64-00018 Russian Federation
CitationJournal: Chem Sci / Year: 2025
Title: Engineering of soluble bacteriorhodopsin.
Authors: Nikolaev, A. / Orlov, Y. / Tsybrov, F. / Kuznetsova, E. / Shishkin, P. / Kuzmin, A. / Mikhailov, A. / Nikolaeva, Y.S. / Anuchina, A. / Chizhov, I. / Semenov, O. / Kapranov, I. / ...Authors: Nikolaev, A. / Orlov, Y. / Tsybrov, F. / Kuznetsova, E. / Shishkin, P. / Kuzmin, A. / Mikhailov, A. / Nikolaeva, Y.S. / Anuchina, A. / Chizhov, I. / Semenov, O. / Kapranov, I. / Borshchevskiy, V. / Remeeva, A. / Gushchin, I.
History
DepositionNov 15, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: soluble bacteriorhodopsin
B: soluble bacteriorhodopsin
C: soluble bacteriorhodopsin
D: soluble bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,61912
Polymers110,0974
Non-polymers1,5228
Water9,008500
1
A: soluble bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9053
Polymers27,5241
Non-polymers3802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: soluble bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9053
Polymers27,5241
Non-polymers3802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: soluble bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0014
Polymers27,5241
Non-polymers4773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: soluble bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8092
Polymers27,5241
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.035, 96.092, 109.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
soluble bacteriorhodopsin


Mass: 27524.291 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium sulfate 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.76→36.2 Å / Num. obs: 76128 / % possible obs: 76.7 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.036 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.76-1.880.9682.538490.6550.311.01922.2
5.36-35.212.50.03338.5379810.010.03499.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
STARANISOdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.76→36.17 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.04 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21253 3687 4.9 %RANDOM
Rwork0.17707 ---
obs0.17884 70884 74.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.259 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.76→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7215 0 20 500 7735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0127612
X-RAY DIFFRACTIONr_bond_other_d00.0167247
X-RAY DIFFRACTIONr_angle_refined_deg0.9081.89210333
X-RAY DIFFRACTIONr_angle_other_deg0.3351.76216896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3255965
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.548567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.423101360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0470.21135
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.028677
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021467
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_it2.1111.573691
X-RAY DIFFRACTIONr_mcbond_other2.1071.573690
X-RAY DIFFRACTIONr_mcangle_it2.9552.8024624
X-RAY DIFFRACTIONr_mcangle_other2.9552.8034625
X-RAY DIFFRACTIONr_scbond_it4.0551.9463921
X-RAY DIFFRACTIONr_scbond_other4.0341.9363906
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2153.3365655
X-RAY DIFFRACTIONr_long_range_B_refined7.62818.89170
X-RAY DIFFRACTIONr_long_range_B_other7.59317.79059
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.803 Å
RfactorNum. reflection% reflection
Rfree0.237 14 -
Rwork0.303 236 -
obs--3.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.838-0.1855-0.0530.33620.08310.2086-0.00040.02240.0391-0.01180.0072-0.0355-0.0053-0.0022-0.00680.01770.0024-0.0030.01640.00880.03140.236633.312813.8722
20.7181-0.05510.07690.2658-0.0310.27060.0419-0.0682-0.14520.0025-0.01770.015-0.0198-0.0497-0.02410.0058-0.0041-0.0040.03130.00960.0641-6.034631.912814.5664
30.7435-0.3383-0.18810.42730.13810.22470.0694-0.03330.0977-0.072-0.0034-0.0868-0.01770.0155-0.0660.0223-0.00780.02990.0225-0.02010.0541-10.6595-18.566912.3087
40.3541-0.0440.04590.4677-0.08610.25640.01390.00840.0130.03290.01150.06530.03810.0132-0.02540.035-0.00340.00020.0104-0.01010.032638.2372-13.018114.2266
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 235
2X-RAY DIFFRACTION2B8 - 231
3X-RAY DIFFRACTION3C7 - 231
4X-RAY DIFFRACTION4D8 - 232

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