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- PDB-7nje: gamma(S)-crystallin 9-site deamidation mutant grown inside HARE s... -

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Basic information

Entry
Database: PDB / ID: 7nje
Titlegamma(S)-crystallin 9-site deamidation mutant grown inside HARE serial crystallography chip
ComponentsGamma-crystallin S
KeywordsSTRUCTURAL PROTEIN / serial crystallography / crystallin / vapour diffusion / silicon chip
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception / morphogenesis of an epithelium
Similarity search - Function
Beta/Gamma crystallin / : / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsNorton-Baker, B. / Mehrabi, P. / Boger, J. / Schonherr, R. / von Stetten, D. / Schikora, H. / Martin, R.W. / Miller, R.J.D. / Redecke, L. / Schulz, E.C.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: A simple vapor-diffusion method enables protein crystallization inside the HARE serial crystallography chip.
Authors: Norton-Baker, B. / Mehrabi, P. / Boger, J. / Schonherr, R. / von Stetten, D. / Schikora, H. / Kwok, A.O. / Martin, R.W. / Miller, R.J.D. / Redecke, L. / Schulz, E.C.
History
DepositionFeb 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-crystallin S
B: Gamma-crystallin S


Theoretical massNumber of molelcules
Total (without water)41,9372
Polymers41,9372
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-3 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.400, 89.200, 111.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 5 through 71 or resid 73 through 178))
d_2ens_1(chain "B" and (resid 5 through 71 or resid 73 through 178))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYGLUA1 - 67
d_12ens_1TRPGLUA70 - 175
d_21ens_1GLYGLUB1 - 67
d_22ens_1TRPGLUB69 - 174

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Components

#1: Protein Gamma-crystallin S / Beta-crystallin S / Gamma-S-crystallin


Mass: 20968.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGS, CRYG8 / Production host: Escherichia coli (E. coli) / References: UniProt: P22914
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 50 mM HEPES pH 7.0, 20% PEG3350, 0.1 M sodium acetate pH 5.45

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jun 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3→69.6 Å / Num. obs: 8132 / % possible obs: 99.96 % / Redundancy: 48 % / Biso Wilson estimate: 52.32 Å2 / CC1/2: 0.9574 / Net I/σ(I): 2.5
Reflection shellResolution: 3→3.108 Å / Num. unique obs: 787 / CC1/2: 0.885
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FD8

6fd8


Resolution: 3→69.6 Å / SU ML: 0.4305 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.481
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2711 361 4.45 %
Rwork0.235 7750 -
obs0.2367 8111 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.64 Å2
Refinement stepCycle: LAST / Resolution: 3→69.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 0 16 2908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352988
X-RAY DIFFRACTIONf_angle_d0.83514031
X-RAY DIFFRACTIONf_chiral_restr0.0554385
X-RAY DIFFRACTIONf_plane_restr0.0056529
X-RAY DIFFRACTIONf_dihedral_angle_d21.70461119
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.798069996017 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.430.41451030.34542529X-RAY DIFFRACTION99.7
3.43-4.330.28061250.22252544X-RAY DIFFRACTION99.7
4.33-69.60.20851330.19212677X-RAY DIFFRACTION99.75

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