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- PDB-5o5s: X-ray crystal structure of the RapZ C-terminal domain from Escher... -

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Basic information

Entry
Database: PDB / ID: 5o5s
TitleX-ray crystal structure of the RapZ C-terminal domain from Escherichia coli
ComponentsRNase adapter protein RapZ
KeywordsCHAPERONE / RNA binding Amino-sugar metabolism Kinase like domain PFK like domain
Function / homology
Function and homology information


RNA destabilization / carbohydrate derivative binding / protein homotetramerization / molecular adaptor activity / GTP binding / protein-containing complex / RNA binding / ATP binding / identical protein binding
Similarity search - Function
RapZ-like family / P-loop ATPase protein family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MALONATE ION / RNase adapter protein RapZ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.17 Å
AuthorsGonzalez, G.M. / Durica-Mitic, S. / Hardwick, S.W. / Moncrieffe, M. / Resch, M. / Neumann, P. / Ficner, R. / Gorke, B. / Luisi, B.F.
Funding support United Kingdom, Austria, 3items
OrganizationGrant numberCountry
Wellcome TrustRG84381 United Kingdom
Austrian Science FundP 26681-B22 Austria
Austrian Science FundF4317 Austria
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural insights into RapZ-mediated regulation of bacterial amino-sugar metabolism.
Authors: Gonzalez, G.M. / Durica-Mitic, S. / Hardwick, S.W. / Moncrieffe, M.C. / Resch, M. / Neumann, P. / Ficner, R. / Gorke, B. / Luisi, B.F.
History
DepositionJun 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNase adapter protein RapZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5532
Polymers15,4511
Non-polymers1021
Water2,324129
1
A: RNase adapter protein RapZ
hetero molecules

A: RNase adapter protein RapZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1054
Polymers30,9012
Non-polymers2042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area2700 Å2
ΔGint-7 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.720, 61.720, 124.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein RNase adapter protein RapZ


Mass: 15450.694 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP Residues 154-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rapZ, yhbJ, b3205, JW3172 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P0A894
#2: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.38 Å3/Da / Density % sol: 48.34 % / Description: Hexagonal
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM HEPES, pH 7.0, 1 M malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.17→62.29 Å / Num. obs: 48089 / % possible obs: 99.57 % / Redundancy: 22.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.5
Reflection shellResolution: 1.17→1.21 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4303 / CC1/2: 0.6 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(dev_2747: ???)refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 1.17→53.451 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.35
RfactorNum. reflection% reflection
Rfree0.1759 2359 4.95 %
Rwork0.1538 --
obs0.1549 47696 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.17→53.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 0 7 129 1139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121066
X-RAY DIFFRACTIONf_angle_d1.2081453
X-RAY DIFFRACTIONf_dihedral_angle_d2.916621
X-RAY DIFFRACTIONf_chiral_restr0.102155
X-RAY DIFFRACTIONf_plane_restr0.009188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.17-1.19390.32991130.3092560X-RAY DIFFRACTION97
1.1939-1.21980.31061350.29052582X-RAY DIFFRACTION98
1.2198-1.24820.30551210.25342571X-RAY DIFFRACTION98
1.2482-1.27940.27391320.24112604X-RAY DIFFRACTION98
1.2794-1.3140.26551420.21082612X-RAY DIFFRACTION99
1.314-1.35270.24911490.18312597X-RAY DIFFRACTION99
1.3527-1.39640.20221430.17212619X-RAY DIFFRACTION99
1.3964-1.44630.19871340.15812659X-RAY DIFFRACTION100
1.4463-1.50420.16951530.13312636X-RAY DIFFRACTION100
1.5042-1.57270.14651310.12072647X-RAY DIFFRACTION100
1.5727-1.65560.14451370.11372682X-RAY DIFFRACTION100
1.6556-1.75930.12231240.12182700X-RAY DIFFRACTION100
1.7593-1.89520.15391220.1192692X-RAY DIFFRACTION100
1.8952-2.08590.14191400.12152722X-RAY DIFFRACTION100
2.0859-2.38770.13791600.13232726X-RAY DIFFRACTION100
2.3877-3.00820.15891430.14862779X-RAY DIFFRACTION100
3.0082-53.50670.17961800.15562949X-RAY DIFFRACTION100

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