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- PDB-1zkm: Structural Analysis of Escherichia Coli ThiF -

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Basic information

Entry
Database: PDB / ID: 1zkm
TitleStructural Analysis of Escherichia Coli ThiF
ComponentsAdenylyltransferase thiF
KeywordsTRANSFERASE / ThiF / ThiS / MoeB / Ubiquitin / Rossmann Fold / P-Loop / ATP binding
Function / homology
Function and homology information


sulfur carrier protein ThiS adenylyltransferase / adenylyltransferase complex / thiazole biosynthetic process / ubiquitin-like modifier activating enzyme activity / sulfurtransferase complex / AMPylase activity / sulfotransferase activity / thiosulfate sulfurtransferase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process ...sulfur carrier protein ThiS adenylyltransferase / adenylyltransferase complex / thiazole biosynthetic process / ubiquitin-like modifier activating enzyme activity / sulfurtransferase complex / AMPylase activity / sulfotransferase activity / thiosulfate sulfurtransferase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / nucleotidyltransferase activity / protein homodimerization activity / zinc ion binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
Thiazole biosynthesis adenylyltransferase ThiF / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sulfur carrier protein ThiS adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.95 Å
AuthorsDuda, D.M. / Walden, H. / Sfondouris, J. / Schulman, B.A.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structural Analysis of Escherichia Coli ThiF.
Authors: Duda, D.M. / Walden, H. / Sfondouris, J. / Schulman, B.A.
History
DepositionMay 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Feb 14, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
Remark 600HETEROGEN ZN 240 IS ASSOCIATED WITH CHAIN A. ZN 241 IS ASSOCIATED WITH CHAIN B. ZN 242 IS ...HETEROGEN ZN 240 IS ASSOCIATED WITH CHAIN A. ZN 241 IS ASSOCIATED WITH CHAIN B. ZN 242 IS ASSOCIATED WITH CHAIN C. ZN 243 IS ASSOCIATED WITH CHAIN D.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylyltransferase thiF
B: Adenylyltransferase thiF
C: Adenylyltransferase thiF
D: Adenylyltransferase thiF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8058
Polymers108,5434
Non-polymers2624
Water00
1
A: Adenylyltransferase thiF
B: Adenylyltransferase thiF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4024
Polymers54,2722
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-34 kcal/mol
Surface area17610 Å2
MethodPISA
2
C: Adenylyltransferase thiF
D: Adenylyltransferase thiF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4024
Polymers54,2722
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-34 kcal/mol
Surface area18070 Å2
MethodPISA
3
A: Adenylyltransferase thiF
B: Adenylyltransferase thiF
C: Adenylyltransferase thiF
D: Adenylyltransferase thiF
hetero molecules

A: Adenylyltransferase thiF
B: Adenylyltransferase thiF
C: Adenylyltransferase thiF
D: Adenylyltransferase thiF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,61016
Polymers217,0878
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_555-y+1/4,-x+1/4,-z+1/41
Buried area29540 Å2
ΔGint-163 kcal/mol
Surface area63140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)360.168, 360.168, 360.168
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
DetailsThe Biological Unit is comprised of a ThiF homodimer consisting of either A/B or C/D.

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Components

#1: Protein
Adenylyltransferase thiF


Mass: 27135.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: thiF / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P30138, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 4.5 Å3/Da / Density % sol: 72.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium Acetate, MES, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.2826, 1.2821, 1.2500
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDMar 15, 2004Pt-coated toroidal Si mirror for horizontal and vertical focussing followed by double flat Si crystal monochromator
ADSC QUANTUM 3152CCDMar 15, 2004Pt-coated toroidal Si mirror for horizontal and vertical focussing followed by double flat Si crystal monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double flat Si crystal monochromatorMADMx-ray1
2double flat Si crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.28261
21.28211
31.251
41.11
ReflectionResolution: 2.95→20 Å / Num. obs: 46923 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.95 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.95→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.28 2038 random
Rwork0.229 --
all-42346 -
obs-40926 -
Refinement stepCycle: LAST / Resolution: 2.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7185 0 4 0 7189
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007943
X-RAY DIFFRACTIONc_angle_deg1.43351

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