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- PDB-3qxx: Crystal structure of dethiobiotin synthetase (BioD) from Helicoba... -

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Basic information

Entry
Database: PDB / ID: 3qxx
TitleCrystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GDP and 8-aminocaprylic acid
ComponentsDethiobiotin synthetase
KeywordsLIGASE / DTBS / dethiobiotin synthetase / Structural Genomics / PSI-BIOLOGY / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


dethiobiotin synthase / dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Dethiobiotin synthase BioD / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
8-aminooctanoic acid / GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / ATP-dependent dethiobiotin synthetase BioD
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsPorebski, P.J. / Klimecka, M.M. / Chruszcz, M. / Murzyn, K. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Febs J. / Year: 2012
Title: Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members.
Authors: Porebski, P.J. / Klimecka, M. / Chruszcz, M. / Nicholls, R.A. / Murzyn, K. / Cuff, M.E. / Xu, X. / Cymborowski, M. / Murshudov, G.N. / Savchenko, A. / Edwards, A. / Minor, W.
History
DepositionMar 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Mar 27, 2013Group: Database references
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dethiobiotin synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,35913
Polymers27,1481
Non-polymers1,21112
Water6,143341
1
A: Dethiobiotin synthetase
hetero molecules

A: Dethiobiotin synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,71726
Polymers54,2962
Non-polymers2,42124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area7460 Å2
ΔGint-76 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.883, 37.845, 68.839
Angle α, β, γ (deg.)90.00, 101.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-380-

HOH

21A-394-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dethiobiotin synthetase / DTB synthetase / DTBS / Dethiobiotin synthase


Mass: 27148.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: bioD, hp0029, HP_0029 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Gold(de3) Magic / References: UniProt: O24872, dethiobiotin synthase

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Non-polymers , 7 types, 353 molecules

#2: Chemical ChemComp-8AC / 8-aminooctanoic acid / 8-aminocaprylic acid


Mass: 159.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO2
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 1.93 Å3/Da / Density % sol: 36.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG3350; 100 MM NH4NO3; 100 MM BIS-TRIS; 5% GLYCEROL; SOAKED WITH 10 MM GDP, 10 MM MGCL2, 10 MM 8-AMINOOCTANOIC ACID; IN SITU PROTEOLYSIS - CHYMOTRYPSIN, pH 5.5, VAPOR DIFFUSION, HANGING ...Details: 20% PEG3350; 100 MM NH4NO3; 100 MM BIS-TRIS; 5% GLYCEROL; SOAKED WITH 10 MM GDP, 10 MM MGCL2, 10 MM 8-AMINOOCTANOIC ACID; IN SITU PROTEOLYSIS - CHYMOTRYPSIN, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jul 11, 2008 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.36→50 Å / Num. all: 43768 / Num. obs: 43768 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 29.5
Reflection shellResolution: 1.36→1.38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1884 / Rsym value: 0.386 / % possible all: 86.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMAC5.5refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QMO

2qmo


Resolution: 1.36→50 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.317 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16171 2205 5 %RANDOM
Rwork0.1296 ---
all0.13125 41560 --
obs0.13125 41560 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.494 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å2-0.71 Å2
2--0.13 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.36→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 76 341 2161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221935
X-RAY DIFFRACTIONr_bond_other_d00.021294
X-RAY DIFFRACTIONr_angle_refined_deg1.6832.0042629
X-RAY DIFFRACTIONr_angle_other_deg3.71933198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1815246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23425.24482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41215340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.452157
X-RAY DIFFRACTIONr_chiral_restr0.1260.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022114
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02361
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0451.51168
X-RAY DIFFRACTIONr_mcbond_other2.2811.5467
X-RAY DIFFRACTIONr_mcangle_it2.78421900
X-RAY DIFFRACTIONr_scbond_it4.0693767
X-RAY DIFFRACTIONr_scangle_it5.5284.5722
X-RAY DIFFRACTIONr_rigid_bond_restr2.331868
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.36→1.396 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 149 -
Rwork0.196 2679 -
obs-2679 86.4 %

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