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- PDB-5o5q: X-ray crystal structure of RapZ from Escherichia coli (P3221 spac... -

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Basic information

Entry
Database: PDB / ID: 5o5q
TitleX-ray crystal structure of RapZ from Escherichia coli (P3221 space group)
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
RNase adapter protein RapZ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 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

Downloads & links

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Assembly

Deposited unit
A: RNase adapter protein RapZ
B: RNase adapter protein RapZ
D: RNase adapter protein RapZ
C: RNase adapter protein RapZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,92019
Polymers135,4794
Non-polymers1,44115
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14710 Å2
ΔGint-323 kcal/mol
Surface area47340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.540, 91.540, 352.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
RNase adapter protein RapZ


Mass: 33869.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rapZ, yhbJ, b3205, JW3172 / Plasmid: pBGG164 / Production host: Escherichia coli (E. coli) / Variant (production host): Z106 / References: UniProt: P0A894
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.51 Å3/Da / Density % sol: 64.95 % / Description: Hexagonal
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M MES,1 M ammonium sulfate, 0.01 M mercaptoethanol, 1%(v/v) glycerol pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.25→45.77 Å / Num. obs: 27399 / % possible obs: 97.6 % / Redundancy: 4.67 % / Biso Wilson estimate: 84.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.37
Reflection shellResolution: 3.25→3.366 Å / Redundancy: 4.77 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 2.56 / CC1/2: 0.768

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Processing

Software
NameVersionClassification
PHENIX(dev_2747: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→45.77 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.26
RfactorNum. reflection% reflection
Rfree0.2729 1371 5 %
Rwork0.2176 --
obs0.2204 27396 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.25→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8083 0 75 2 8160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048304
X-RAY DIFFRACTIONf_angle_d0.73411293
X-RAY DIFFRACTIONf_dihedral_angle_d7.9184996
X-RAY DIFFRACTIONf_chiral_restr0.0481301
X-RAY DIFFRACTIONf_plane_restr0.0091462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2502-3.36640.39661210.32772295X-RAY DIFFRACTION88
3.3664-3.50110.31871250.25292379X-RAY DIFFRACTION91
3.5011-3.66040.30381380.24342615X-RAY DIFFRACTION100
3.6604-3.85330.29071370.21862610X-RAY DIFFRACTION100
3.8533-4.09460.27111380.20912624X-RAY DIFFRACTION100
4.0946-4.41050.26391400.19582644X-RAY DIFFRACTION100
4.4105-4.85390.2181400.17292651X-RAY DIFFRACTION100
4.8539-5.55520.25331390.18562645X-RAY DIFFRACTION100
5.5552-6.99490.30141430.25962735X-RAY DIFFRACTION100
6.9949-45.77450.26641500.21892827X-RAY DIFFRACTION98
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)
10.78050.7377-0.81741.4099-1.09982.3927-0.23590.3594-0.3908-0.36330.2657-0.17740.6046-0.0985-0.13370.84640.21050.2410.4022-0.15240.665363.94284.525414.2191
20.7538-0.57750.56282.0621-1.3531.90970.1513-0.3067-0.24710.7556-0.09990.2298-0.2985-0.20840.18011.01360.2980.33540.60450.0850.596554.681611.08548.4158
31.6556-0.575-0.95491.6999-0.33091.0250.26270.2180.69860.0537-0.0063-0.3429-0.6428-0.0665-0.05941.24790.47620.31290.44260.03910.742259.262641.665517.5845
42.6379-1.3925-0.08331.48410.1961.2842-0.1199-0.1114-0.44410.32340.08840.95990.1693-0.56120.08091.06070.42080.29180.74430.03970.8528.79538.725235.7501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq -1:280)
2X-RAY DIFFRACTION2(chain B and resseq 4:280)
3X-RAY DIFFRACTION3(chain D and resseq -3:281)
4X-RAY DIFFRACTION4(chain C and resseq 1:281)

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