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- PDB-9v5c: Light driven bicarbonate reduction by fluorescent protein mRuby-Metha1 -

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Basic information

Entry
Database: PDB / ID: 9v5c
TitleLight driven bicarbonate reduction by fluorescent protein mRuby-Metha1
Componentsfluorescent protein mRuby
KeywordsFLUORESCENT PROTEIN / fluorescent protein mRuby
Function / homologyphenylmethanol
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsDong, J.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900913 China
CitationJournal: To Be Published
Title: Observation of light driven CO2 photoreduction by fluorescent protein mRuby
Authors: Dong, J.S.
History
DepositionMay 25, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fluorescent protein mRuby
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6772
Polymers24,5691
Non-polymers1081
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.400, 95.530, 31.770
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 fluorescent protein mRuby


Mass: 24569.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-010 / phenylmethanol


Mass: 108.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M NH4HCO3, 0.1M Bistris pH6.5, 25%PEG3350

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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: Oct 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.68→31.77 Å / Num. obs: 24095 / % possible obs: 99.7 % / Redundancy: 12.7 % / CC1/2: 0.996 / Net I/σ(I): 9
Reflection shellResolution: 1.68→1.72 Å / Num. unique obs: 1732 / CC1/2: 0.293

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→30.16 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.894 / SU B: 6.953 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 1184 4.9 %RANDOM
Rwork0.23103 ---
obs0.23262 22874 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3---0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.68→30.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 2 56 1777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0121824
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161697
X-RAY DIFFRACTIONr_angle_refined_deg1.331.6592462
X-RAY DIFFRACTIONr_angle_other_deg0.4411.5733925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.755232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.791511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32610322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022155
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02433
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_it0.8641.21910
X-RAY DIFFRACTIONr_mcbond_other0.8641.21911
X-RAY DIFFRACTIONr_mcangle_it1.4512.1691146
X-RAY DIFFRACTIONr_mcangle_other1.452.1691147
X-RAY DIFFRACTIONr_scbond_it1.3371.403914
X-RAY DIFFRACTIONr_scbond_other1.3371.404915
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2372.491317
X-RAY DIFFRACTIONr_long_range_B_refined3.29112.061877
X-RAY DIFFRACTIONr_long_range_B_other3.27412.041868
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 80 -
Rwork0.35 1645 -
obs--100 %

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