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- PDB-1nij: YJIA PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1nij
TitleYJIA PROTEIN
ComponentsHypothetical protein yjiAHypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / P-LOOP PROTEIN / GTP BINDING / Structure 2 Function Project / S2F
Function / homology
Function and homology information


transition metal ion binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / DNA damage response / GTP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Hypothetical Protein Yjia; Chain: A;domain 2 / CobW-like, C-terminal domain / Cobalamin synthesis protein cobW C-terminal domain / Cobalamin (vitamin B12) biosynthesis CobW-like, C-terminal / CobW-like, C-terminal domain superfamily / Cobalamin synthesis protein cobW C-terminal domain / CobW/HypB/UreG, nucleotide-binding domain / CobW/HypB/UreG, nucleotide-binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...Hypothetical Protein Yjia; Chain: A;domain 2 / CobW-like, C-terminal domain / Cobalamin synthesis protein cobW C-terminal domain / Cobalamin (vitamin B12) biosynthesis CobW-like, C-terminal / CobW-like, C-terminal domain superfamily / Cobalamin synthesis protein cobW C-terminal domain / CobW/HypB/UreG, nucleotide-binding domain / CobW/HypB/UreG, nucleotide-binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKhil, P.P. / Obmolova, G. / Teplyakov, A. / Howard, A.J. / Gilliland, G.L. / Camerini-Otero, R.D. / Structure 2 Function Project (S2F)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of the Escherichia coli YjiA protein suggests a GTP-dependent regulatory function.
Authors: Khil, P.P. / Obmolova, G. / Teplyakov, A. / Howard, A.J. / Gilliland, G.L. / Camerini-Otero, R.D.
History
DepositionDec 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Hypothetical protein yjiA


Theoretical massNumber of molelcules
Total (without water)35,6971
Polymers35,6971
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.830, 66.520, 56.150
Angle α, β, γ (deg.)90.00, 114.96, 90.00
Int Tables number5
Space group name H-MC121
DetailsMonomer in solution (gel filtration)

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Components

#1: Protein Hypothetical protein yjiA / Hypothesis


Mass: 35696.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YJIA OR B4352 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P24203
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1M Lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MHEPES1reservoirpH7.5
21 Mlithium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.0093, 0.9794, 0.9796, 0.9649
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 16, 2002 / Details: cylindrical glass mirror with Pt and Pd coatings
RadiationMonochromator: Si (111) double-crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00931
20.97941
30.97961
40.96491
ReflectionResolution: 2→26 Å / Num. all: 18965 / Num. obs: 18965 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 16.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1173 / % possible all: 92.8
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 21164 / % possible obs: 98.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.034
Reflection shell
*PLUS
Mean I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2→10 Å / Cor.coef. Fo:Fc: 0.943 / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rwork0.223 ---
all0.223 18703 --
obs0.223 18703 100 %-
Rfree---NA
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.69 Å20 Å2-0.43 Å2
2--1.04 Å20 Å2
3---1.29 Å2
Refine analyzeLuzzati coordinate error obs: 0.268 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 0 166 2664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212543
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.9593447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985316
X-RAY DIFFRACTIONr_chiral_restr0.1250.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021922
X-RAY DIFFRACTIONr_nbd_refined0.2980.21300
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.2172
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3680.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2810.212
X-RAY DIFFRACTIONr_mcbond_it8.72541572
X-RAY DIFFRACTIONr_mcangle_it11.20682538
X-RAY DIFFRACTIONr_scbond_it14.7378971
X-RAY DIFFRACTIONr_scangle_it14.8128909
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.278 1327
Refinement
*PLUS
% reflection Rfree: 3 % / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.1

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