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- PDB-4ixn: Crystal Structure of Zn(II)-bound E37A,C66A,C67A triple mutant Yj... -

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Basic information

Entry
Database: PDB / ID: 4ixn
TitleCrystal Structure of Zn(II)-bound E37A,C66A,C67A triple mutant YjiA GTPase
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 ...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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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: 2.05 Å
AuthorsJost, M. / 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 1.7Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _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.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_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: Uncharacterized GTP-binding protein YjiA
B: Uncharacterized GTP-binding protein YjiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5377
Polymers71,1492
Non-polymers3885
Water4,612256
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-105 kcal/mol
Surface area27340 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)71,5377
Polymers71,1492
Non-polymers3885
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3210 Å2
ΔGint-98 kcal/mol
Surface area27040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.071, 68.436, 77.699
Angle α, β, γ (deg.)90.00, 104.23, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE IS NOT KNOWN CRYSTAL STRUCTURE LIKELY CONTAINS A DIMER, BUT ZN(II)-BOUND PROTEIN OLIGOMERIZES IN SOLUTION, AS INDICATED BY SIZE EXCLUSION CHROMATOGRAPHY. PHYSIOLOGICAL OLIGOMERIZATION STATE UNKNOWN

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Components

#1: Protein Uncharacterized GTP-binding protein YjiA


Mass: 35574.445 Da / Num. of mol.: 2 / Mutation: E37A, C66A, C67A
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.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.03 Å3/Da / Density % sol: 39.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5 uL of 12.4 mg/mL triple mutant YjiA in 0.1 M NaCl, 1 mM TCEP, 25 mM HEPES, mixed with 0.3 uL 0.1 M CaCl2 and 1.5 uL 1.3 M ammonium sulfate, 0.1 M HEPES , pH 7.5, VAPOR DIFFUSION, HANGING ...Details: 1.5 uL of 12.4 mg/mL triple mutant YjiA in 0.1 M NaCl, 1 mM TCEP, 25 mM HEPES, mixed with 0.3 uL 0.1 M CaCl2 and 1.5 uL 1.3 M ammonium sulfate, 0.1 M HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2012
RadiationMonochromator: Si(111) cryo-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→75.3 Å / Num. all: 35715 / Num. obs: 35715 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rsym value: 0.085 / Net I/σ(I): 18.6
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1784 / Rsym value: 0.59 / % possible all: 98.8

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Processing

Software
NameVersionClassification
APSconsoledata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→75.3 Å / SU ML: 0.24 / Isotropic thermal model: isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 1747 4.95 %same as for Zn(II)-soaked WT YjiA between 30 and 2.57 A resolution, random for remainder
Rwork0.2027 ---
obs0.2044 35309 98.31 %-
all-35309 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.79 Å2
Refinement stepCycle: LAST / Resolution: 2.05→75.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4811 0 13 256 5080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084986
X-RAY DIFFRACTIONf_angle_d0.7276782
X-RAY DIFFRACTIONf_dihedral_angle_d11.381778
X-RAY DIFFRACTIONf_chiral_restr0.049803
X-RAY DIFFRACTIONf_plane_restr0.003888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.11030.29641400.25562790X-RAY DIFFRACTION99
2.1103-2.17850.32481360.24772787X-RAY DIFFRACTION99
2.1785-2.25630.28471460.23852822X-RAY DIFFRACTION99
2.2563-2.34670.26841330.22592779X-RAY DIFFRACTION97
2.3467-2.45350.26041500.23472787X-RAY DIFFRACTION99
2.4535-2.58280.26911450.22192797X-RAY DIFFRACTION99
2.5828-2.74470.24981650.21512768X-RAY DIFFRACTION98
2.7447-2.95660.24911220.22242806X-RAY DIFFRACTION98
2.9566-3.25410.24221360.2092813X-RAY DIFFRACTION99
3.2541-3.7250.20521600.18042775X-RAY DIFFRACTION98
3.725-4.6930.2151600.1652835X-RAY DIFFRACTION99
4.693-75.36510.22141540.19842803X-RAY DIFFRACTION96
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)
12.5477-0.3702-0.03783.683-1.34344.3439-0.0464-0.6708-0.48340.39590.1090.06460.2299-0.4405-0.01340.4002-0.0299-0.03520.50580.11030.324823.20127.848128.0714
22.74740.11760.55542.74920.5663.4048-0.075-0.00850.1904-0.1450.10220.0001-0.0881-0.1563-0.04870.20940.0008-0.01120.14480.030.201823.110722.12756.1208
33.4920.2066-1.14364.36251.60354.166-0.13050.2676-0.1709-0.1890.0378-0.06750.13080.02050.10280.25850.0142-0.02490.2726-0.00820.212950.46676.75789.703
42.08050.49140.19663.20880.97393.6871-0.0488-0.08540.15910.50650.0625-0.120.21570.07510.02090.25420.0167-0.01410.1915-0.01290.178151.069721.335131.5267
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 1:123)
4X-RAY DIFFRACTION4(chain 'B' and resseq 124:318)

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