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- PDB-2gem: 2.1A crystal structure of Salmonella tyhpimurium YeaZ, a putative... -

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Basic information

Entry
Database: PDB / ID: 2gem
Title2.1A crystal structure of Salmonella tyhpimurium YeaZ, a putative Gram-negative RPF, form-A
ComponentsPutative Gram negative resuscitation promoting factor
KeywordsCHAPERONE / M22 / glycoprotease / yeaZ / actin-like-fold
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine modification / cytosol
Similarity search - Function
tRNA threonylcarbamoyl adenosine modification protein TsaB / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsNichols, C.E. / Stammers, D.K.
CitationJournal: Proteins / Year: 2006
Title: Structural Characterization of Salmonella typhimurium YeaZ, an M22 O-Sialoglycoprotein Endopeptidase Homolog
Authors: Nichols, C.E. / Johnson, C. / Lockyer, M. / Charles, I.G. / Lamb, H.K. / Hawkins, A.R. / Stammers, D.K.
History
DepositionMar 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: reflns / software / Item: _reflns.percent_possible_obs
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative Gram negative resuscitation promoting factor
B: Putative Gram negative resuscitation promoting factor


Theoretical massNumber of molelcules
Total (without water)49,5322
Polymers49,5322
Non-polymers00
Water7,260403
1
A: Putative Gram negative resuscitation promoting factor

A: Putative Gram negative resuscitation promoting factor


Theoretical massNumber of molelcules
Total (without water)49,5322
Polymers49,5322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
2
B: Putative Gram negative resuscitation promoting factor

B: Putative Gram negative resuscitation promoting factor


Theoretical massNumber of molelcules
Total (without water)49,5322
Polymers49,5322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)40.700, 40.700, 464.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsAsymetric unit dimer and putative biological dimer are equivalent

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Components

#1: Protein Putative Gram negative resuscitation promoting factor


Mass: 24766.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: SL3261 / Gene: yegS,YeaZ / Plasmid: pMUT101 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7CQE0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 22% PEG3350 + 0.2M Sodium Malonate, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1410.89843, 0.97925
SYNCHROTRONESRF ID14-120.934
Detector
TypeIDDetectorDateDetails
MARMOSAIC 225 mm CCD1CCDJul 23, 2004mirrors
ADSC QUANTUM 42CCDAug 6, 2004Beryllium compound refractive lenses + diamond monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MirrorsMADMx-ray1
2DiamondSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.898431
20.979251
30.9341
ReflectionResolution: 2.1→30 Å / Num. all: 23568 / Num. obs: 28024 / Observed criterion σ(I): -2 / Redundancy: 3.3 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 28.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1188 / % possible all: 44

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Processing

Software
NameVersionClassification
ProDCdata collection
DENZOdata reduction
SOLVEphasing
CNS1.1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.11 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2526793.24 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: native data was used for refinement and was solved by transferring output model/phases from RESOLVE which were generated from a different almost isomorphous SeMet crystal.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2323 9.9 %Random
Rwork0.22 ---
all0.247 23568 --
obs0.22 28024 84.1 %-
Displacement parametersBiso mean: 42.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å20.37 Å20 Å2
2--2.3 Å20 Å2
3----4.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 0 403 3627
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.41 116 9.8 %
Rwork0.378 1072 -
obs-1188 44.2 %

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