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- PDB-7xhs: Crystal structure of CipA crystal produced by cell-free protein s... -

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Basic information

Entry
Database: PDB / ID: 7xhs
TitleCrystal structure of CipA crystal produced by cell-free protein synthesis
ComponentsCro/Cl family transcriptional regulator
KeywordsCrystalline inclusion protein / in cell crystal
Function / homologyCro/Cl family transcriptional regulator
Function and homology information
Biological speciesPhotorhabdus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsAbe, S. / Tanaka, J. / Kojima, M. / Kanamaru, S. / Yamashita, K. / Hirata, K. / Ueno, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18H05421 Japan
Japan Society for the Promotion of Science (JSPS)JP19H02830 Japan
Japan Science and TechnologyJPMJTR20U1 Japan
CitationJournal: Sci Rep / Year: 2022
Title: Cell-free protein crystallization for nanocrystal structure determination.
Authors: Abe, S. / Tanaka, J. / Kojima, M. / Kanamaru, S. / Hirata, K. / Yamashita, K. / Kobayashi, A. / Ueno, T.
History
DepositionApr 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cro/Cl family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)11,7341
Polymers11,7341
Non-polymers00
Water36020
1
A: Cro/Cl family transcriptional regulator

A: Cro/Cl family transcriptional regulator

A: Cro/Cl family transcriptional regulator

A: Cro/Cl family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)46,9374
Polymers46,9374
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area8460 Å2
ΔGint-60 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.090, 61.090, 54.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

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Components

#1: Protein Cro/Cl family transcriptional regulator


Mass: 11734.304 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus (bacteria) / Gene: C6H68_06435 / Production host: Triticum aestivum (bread wheat) / References: UniProt: A0A2S8QTL8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 293 K / Method: small tubes / Details: cell-free protein crystallization

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 5781 / % possible obs: 100 % / Redundancy: 19.3 % / Biso Wilson estimate: 26.65 Å2 / CC1/2: 0.994 / Net I/σ(I): 9.04
Reflection shellResolution: 2.11→2.24 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5781 / CC1/2: 0.587

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata scaling
Cootmodel building
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→43.2 Å / SU ML: 0.2462 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.2689
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2224 579 10.02 %
Rwork0.1869 5202 -
obs0.1905 5781 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.38 Å2
Refinement stepCycle: LAST / Resolution: 2.11→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms718 0 0 20 738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009725
X-RAY DIFFRACTIONf_angle_d1.1588970
X-RAY DIFFRACTIONf_chiral_restr0.0596118
X-RAY DIFFRACTIONf_plane_restr0.0042116
X-RAY DIFFRACTIONf_dihedral_angle_d6.903996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.320.33491430.25931293X-RAY DIFFRACTION99.51
2.32-2.660.24371480.1971284X-RAY DIFFRACTION100
2.66-3.350.24611400.21381301X-RAY DIFFRACTION100
3.35-43.20.17461480.15091324X-RAY DIFFRACTION100

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