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- PDB-5o5o: X-ray crystal structure of RapZ from Escherichia coli (P32 space ... -

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Basic information

Entry
Database: PDB / ID: 5o5o
TitleX-ray crystal structure of RapZ from Escherichia coli (P32 space group)
ComponentsRNase adapter protein RapZ
KeywordsCHAPERONE / RNA binding Amino-sugar metabolism Kinase like domain PFK like domain
Function / homologyP-loop containing nucleoside triphosphate hydrolase / RapZ-like family / P-loop ATPase protein family / RNA processing / GTP binding / RNA binding / ATP binding / identical protein binding / RNase adapter protein RapZ
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.404 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.
Validation Report
SummaryFull reportAbout validation report
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
C: RNase adapter protein RapZ
D: RNase adapter protein RapZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,30616
Polymers130,1534
Non-polymers1,15312
Water1448
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13500 Å2
ΔGint-265 kcal/mol
Surface area47270 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)92.750, 92.750, 156.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein/peptide
RNase adapter protein RapZ


Mass: 32538.320 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P0A894
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4 / Sulfate
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 3.17 Å3/Da / Density % sol: 61.25 % / Description: Hexagonal
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M MES, 1.1 M ammonium sulfate, 0.01 M beta-mercaptoethanol, 1 percent glycerol, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.4→46.33 Å / Num. obs: 20540 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 71.8 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.2
Reflection shellResolution: 3.4→3.48 Å / Redundancy: 3.58 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.695 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2747: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.404→46.33 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 26.98
RfactorNum. reflection% reflection
Rfree0.2663 2053 10 %
Rwork0.1973 --
Obs0.2041 20535 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.404→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8180 0 60 8 8248
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0118399
f_angle_d1.32311435
f_dihedral_angle_d9.5215052
f_chiral_restr0.071321
f_plane_restr0.011478
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4043-3.48340.35281320.2666119396
3.4834-3.57050.36591390.2518125299
3.5705-3.6670.30021320.2466118199
3.667-3.77490.29721380.24081242100
3.7749-3.89670.33951360.22841232100
3.8967-4.03580.28271400.20541261100
4.0358-4.19730.27381380.21341238100
4.1973-4.38820.26891350.19341214100
4.3882-4.61940.2441400.17411257100
4.6194-4.90850.25951400.1721259100
4.9085-5.2870.26631320.18471196100
5.287-5.81810.29761400.20541259100
5.8181-6.65790.28311390.20911251100
6.6579-8.38020.24331370.19431227100
8.3802-46.37930.17891350.1516122099

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