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- PDB-1zfn: Structural Analysis of Escherichia coli ThiF -

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Basic information

Entry
Database: PDB / ID: 1zfn
TitleStructural Analysis of Escherichia coli ThiF
ComponentsAdenylyltransferase thiF
KeywordsTRANSFERASE / Rossmann Fold / P-LOOP / ATP-Binding / Adenylation / ThiS / ThiF
Function / homology
Function and homology information


sulfur carrier protein ThiS adenylyltransferase / adenylyltransferase complex / sulfurtransferase complex / thiazole biosynthetic process / ubiquitin-like modifier activating enzyme activity / AMPylase activity / sulfotransferase activity / thiosulfate sulfurtransferase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process ...sulfur carrier protein ThiS adenylyltransferase / adenylyltransferase complex / sulfurtransferase complex / thiazole biosynthetic process / ubiquitin-like modifier activating enzyme activity / AMPylase activity / sulfotransferase activity / thiosulfate sulfurtransferase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / nucleotidyltransferase activity / protein homodimerization activity / zinc ion binding / ATP binding / cytosol / cytoplasm
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
ADENOSINE-5'-TRIPHOSPHATE / Sulfur carrier protein ThiS adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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
DepositionApr 20, 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 1.4Nov 19, 2014Group: Derived calculations
Revision 1.5Feb 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_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_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_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

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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)110,83412
Polymers108,5434
Non-polymers2,2908
Water0
1
A: Adenylyltransferase thiF
B: Adenylyltransferase thiF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4176
Polymers54,2722
Non-polymers1,1454
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-31 kcal/mol
Surface area17280 Å2
MethodPISA
2
C: Adenylyltransferase thiF
D: Adenylyltransferase thiF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4176
Polymers54,2722
Non-polymers1,1454
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-33 kcal/mol
Surface area17400 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

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


Theoretical massNumber of molelcules
Total (without water)332,50136
Polymers325,63012
Non-polymers6,87124
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554-z,-x+1/2,y-1/21
crystal symmetry operation10_555-y+1/2,z+1/2,-x1
Buried area52210 Å2
ΔGint-236 kcal/mol
Surface area92770 Å2
MethodPISA
4
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)221,66724
Polymers217,0878
Non-polymers4,58116
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_555-y+1/4,-x+1/4,-z+1/41
Buried area35520 Å2
ΔGint-156 kcal/mol
Surface area61130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)360.3, 360.3, 360.3
Angle α, β, γ (deg.)90, 90, 90
Int Tables number210
Space group name H-MF4132
DetailsThe biological unit is a dimer made of either AB or CD

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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 / Production host: Escherichia coli (E. coli)
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
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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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: 4.5 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium Acetate, MES, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 31, 2004
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. all: 57955 / Num. obs: 52090 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.75→2.87 Å / % possible all: 98.6

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.268 2569 RANDOM
Rwork0.247 --
all-52090 -
obs-50540 -
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7187 0 128 0 7315
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.43
LS refinement shellResolution: 2.75→2.87 Å

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