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- PDB-4ixm: Crystal structure of Zn(II)-bound YjiA GTPase from E. coli -

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Basic information

Entry
Database: PDB / ID: 4ixm
TitleCrystal structure of Zn(II)-bound YjiA GTPase from E. coli
ComponentsUncharacterized GTP-binding protein YjiA
KeywordsHYDROLASE / P-loop GTPase / G-protein / metal homeostasis
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 / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsJost, M. / Ryan, K.S. / Turo, K.E. / Drennan, C.L.
CitationJournal: Biochemistry / Year: 2013
Title: Metal binding properties of Escherichia coli YjiA, a member of the metal homeostasis-associated COG0523 family of GTPases.
Authors: Sydor, A.M. / Jost, M. / Ryan, K.S. / Turo, K.E. / Douglas, C.D. / Drennan, C.L. / Zamble, D.B.
History
DepositionJan 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Jun 12, 2013Group: Database references
Revision 1.3Jul 3, 2013Group: Database references
Revision 1.4Jul 24, 2013Group: Database references
Revision 1.5Jan 1, 2014Group: Database references
Revision 1.6Mar 5, 2014Group: Database references
Revision 1.7Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Uncharacterized GTP-binding protein YjiA
B: Uncharacterized GTP-binding protein YjiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9129
Polymers71,3932
Non-polymers5197
Water77543
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-178 kcal/mol
Surface area27410 Å2
MethodPISA
2
A: Uncharacterized GTP-binding protein YjiA
hetero molecules

B: Uncharacterized GTP-binding protein YjiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9129
Polymers71,3932
Non-polymers5197
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3400 Å2
ΔGint-173 kcal/mol
Surface area26910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.295, 68.869, 77.829
Angle α, β, γ (deg.)90.00, 104.09, 90.00
Int Tables number4
Space group name H-MP1211
DetailsCRYSTAL STRUCTURE LIKELY CONTAINS A DIMER, BUT ZN(II)-BOUND PROTEIN OLIGOMERIZES IN SOLUTION, AS INDICATED BY SIZE EXCLUSION CHROMATOGRAPHY

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Components

#1: Protein Uncharacterized GTP-binding protein YjiA


Mass: 35696.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b4352, JW5790, yjiA / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P24203
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.05 Å3/Da / Density % sol: 39.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 1.5 uL of 13.2 mg/mL YjiA in 0.1 M NaCl, 25 mM HEPES, pH 7.6, mixed with 0.3 uL 0.1 M CaCl2 and 1.5 uL 1.55 M ammonium sulfate, 0.1 M , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.1808 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 21, 2007
RadiationMonochromator: Si(111) Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 2.57→30 Å / Num. all: 35529 / Num. obs: 35529 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.079 / Net I/σ(I): 18.3
Reflection shellResolution: 2.57→2.61 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 1535 / Rsym value: 0.412 / % possible all: 84.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NIJ

1nij


Resolution: 2.57→29.126 Å / SU ML: 0.35 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.67 / Stereochemistry target values: ML
Details: pseudo-translational symmetry. anomalous differences used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 940 5.13 %random
Rwork0.2199 ---
obs0.2221 35283 97.46 %-
all-35283 --
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.69 Å2
Refinement stepCycle: LAST / Resolution: 2.57→29.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4821 0 15 43 4879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024922
X-RAY DIFFRACTIONf_angle_d0.566684
X-RAY DIFFRACTIONf_dihedral_angle_d9.791752
X-RAY DIFFRACTIONf_chiral_restr0.039789
X-RAY DIFFRACTIONf_plane_restr0.002874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.63950.37481760.31422619X-RAY DIFFRACTION100
2.6395-2.71710.30021520.27962614X-RAY DIFFRACTION100
2.7171-2.80470.32381280.26892674X-RAY DIFFRACTION100
2.8047-2.90490.31341030.27482639X-RAY DIFFRACTION100
2.9049-3.02110.29711290.26262670X-RAY DIFFRACTION100
3.0211-3.15840.32991240.2632659X-RAY DIFFRACTION100
3.1584-3.32470.31111380.24562613X-RAY DIFFRACTION100
3.3247-3.53270.22191550.23292638X-RAY DIFFRACTION100
3.5327-3.80490.30451060.24371836X-RAY DIFFRACTION70
3.8049-4.18680.26081580.20082603X-RAY DIFFRACTION100
4.1868-4.79030.22521290.16062656X-RAY DIFFRACTION100
4.7903-6.02650.2281750.19662619X-RAY DIFFRACTION100
6.0265-29.1280.2221310.19562544X-RAY DIFFRACTION97
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)
14.5381-0.07970.09754.9885-1.09617.1765-0.0526-0.7947-0.39770.41640.03490.06290.5118-0.4562-0.00230.5622-0.0422-0.05850.6050.06240.566223.13117.290828.3948
22.3068-0.3440.30192.11330.40193.8992-0.01130.03670.1854-0.16520.0340.0133-0.001-0.2514-0.02930.37990.0014-0.01840.33530.02820.490823.340821.97476.1057
34.20420.6877-1.49053.56190.90265.9511-0.10040.413-0.2666-0.1313-0.0165-0.03320.36940.35170.12770.51490.0738-0.05850.5265-0.03820.522550.73746.27029.5549
41.65590.5899-0.04772.41440.696.2327-0.0270.02130.15280.39670.034-0.02520.31230.2385-0.01560.4449-0.0084-0.0370.4215-0.01170.522251.359921.420631.5234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resseq 1:123)
2X-RAY DIFFRACTION2(chain 'A' and resseq 124:318)
3X-RAY DIFFRACTION3(chain 'B' and resseq 2:123)
4X-RAY DIFFRACTION4(chain 'B' and resseq 124:318)

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