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- PDB-1nrk: YGFZ PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1nrk
TitleYGFZ PROTEIN
ComponentsYGFZ Protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / YGFZ / Structure 2 Function Project / S2F
Function / homology
Function and homology information


RNA modification / folic acid binding / tRNA processing / iron-sulfur cluster assembly / cytosol / cytoplasm
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #160 / Alpha-Beta Plaits - #1630 / tRNA-modifying protein YgfZ / : / YgfZ, beta-barrel domain / YgfZ/GcvT conserved site / YgfZ/GcvT / Aminomethyltransferase beta-barrel domains / Glycine cleavage T-protein/YgfZ, C-terminal / Aminomethyltransferase, folate-binding domain ...Elongation Factor Tu (Ef-tu); domain 3 - #160 / Alpha-Beta Plaits - #1630 / tRNA-modifying protein YgfZ / : / YgfZ, beta-barrel domain / YgfZ/GcvT conserved site / YgfZ/GcvT / Aminomethyltransferase beta-barrel domains / Glycine cleavage T-protein/YgfZ, C-terminal / Aminomethyltransferase, folate-binding domain / Aminomethyltransferase folate-binding domain / Elongation Factor Tu (Ef-tu); domain 3 / Alpha-Beta Plaits / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
tRNA-modifying protein YgfZ / tRNA-modifying protein YgfZ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsTeplyakov, A. / Obmolova, G. / Gilliland, G.L. / Structure 2 Function Project (S2F)
CitationJournal: J.Bacteriol. / Year: 2004
Title: Crystal structure of the YgfZ protein from Escherichia coli suggests a folate-dependent regulatory role in one-carbon metabolism.
Authors: Teplyakov, A. / Obmolova, G. / Sarikaya, E. / Pullalarevu, S. / Krajewski, W. / Galkin, A. / Howard, A.J. / Herzberg, O. / Gilliland, G.L.
History
DepositionJan 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YGFZ Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9473
Polymers36,7551
Non-polymers1922
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.000, 151.000, 68.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein YGFZ Protein / Spot PR51


Mass: 36755.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YGFZ OR B2898 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P39179, UniProt: P0ADE8*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 5.79 Å3/Da / Density % sol: 78.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M Na Acetate, 30% Ammonium Sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
230 %satammonium sulfate1reservoir
30.1 Msodium acetate1reservoirpH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 12, 2002 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 21998 / Num. obs: 21998 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 71.3 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2412 / % possible all: 97.1
Reflection shell
*PLUS
% possible obs: 97.1 % / Num. unique obs: 2412 / Rmerge(I) obs: 0.44

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→10 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.468 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.298 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25179 1106 5.1 %RANDOM
Rwork0.19285 ---
all0.19592 20431 --
obs0.19592 20431 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 64.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.264 Å0.298 Å
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 10 215 2761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212594
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9573516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2965324
X-RAY DIFFRACTIONr_chiral_restr0.1040.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021972
X-RAY DIFFRACTIONr_nbd_refined0.3170.21341
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2182
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3240.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.25
X-RAY DIFFRACTIONr_mcbond_it4.57141619
X-RAY DIFFRACTIONr_mcangle_it7.67482590
X-RAY DIFFRACTIONr_scbond_it8.7418975
X-RAY DIFFRACTIONr_scangle_it10.3848926
LS refinement shellResolution: 2.804→2.871 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.46 72
Rwork0.398 1353
Software
*PLUS
Version: 5.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / % reflection Rfree: 3 % / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.6

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