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

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Basic information

Entry
Database: PDB / ID: 3qxs
TitleCrystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ANP
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / NITRATE ION / ATP-dependent dethiobiotin synthetase BioD
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsKlimecka, M.M. / Porebski, P.J. / Chruszcz, M. / Jablonska, K. / 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.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)28,42315
Polymers27,1481
Non-polymers1,27514
Water5,693316
1
A: Dethiobiotin synthetase
hetero molecules

A: Dethiobiotin synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,84730
Polymers54,2962
Non-polymers2,55128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area7610 Å2
ΔGint4 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.085, 37.582, 69.232
Angle α, β, γ (deg.)90.00, 101.28, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-353-

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 , 5 types, 330 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 36.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% PEG3350; 100 MM NH4NO3; 100 MM BIS-TRIS; SOAKED WITH 10 MM ANP, 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: 1.35→50 Å / Num. all: 44773 / Num. obs: 44773 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.035 / Rsym value: 0.035 / Net I/σ(I): 46.8
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.108 / Mean I/σ(I) obs: 10.5 / Num. unique all: 1906 / Rsym value: 0.108 / % possible all: 83.8

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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: 1.35→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.373 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16519 2261 5.1 %RANDOM
Rwork0.14338 ---
all0.14443 42490 --
obs0.14443 42490 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.605 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.34 Å2
2---0.22 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 80 316 2146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222000
X-RAY DIFFRACTIONr_bond_other_d0.0020.021336
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.9962722
X-RAY DIFFRACTIONr_angle_other_deg2.28833303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9565260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37325.28787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27715352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.193157
X-RAY DIFFRACTIONr_chiral_restr0.1230.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022217
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02377
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_it0.961.51206
X-RAY DIFFRACTIONr_mcbond_other0.1861.5479
X-RAY DIFFRACTIONr_mcangle_it1.65921966
X-RAY DIFFRACTIONr_scbond_it2.6213794
X-RAY DIFFRACTIONr_scangle_it3.7774.5745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 139 -
Rwork0.22 2734 -
obs-2734 85.35 %
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)
10.6512-0.1704-0.21470.58690.06550.96080.0035-0.0574-0.03240.04640.0069-0.01620.07840.0367-0.01030.027-0.0129-0.00440.07370.00420.0414.795-21.162-14.062
21.3672-0.25810.64140.4558-0.13220.89760.0194-0.1343-0.15740.03710.00760.03270.1601-0.051-0.02690.0481-0.01870.01030.07970.01820.0427.347-26.264-8.266
32.78461.43450.64951.49950.75791.12270.0747-0.32710.26360.2077-0.21220.23140.1516-0.22570.13760.0429-0.03170.02720.1105-0.0390.063-3.907-15.595-10.55
40.4922-0.08040.11720.15440.05370.72170.0075-0.03140.0425-0.0005-0.0060.0105-0.0462-0.0114-0.00150.0316-0.0149-0.00320.055-0.00440.052111.195-13.353-21.736
50.53650.3027-0.03251.8561-0.08971.73540.03780.03370.0211-0.1145-0.01860.0999-0.01710.1288-0.01920.0287000.08460.00420.071523.246-19.975-36.561
61.1040.2196-0.05524.58092.32463.24010.0471-0.1280.08260.09340.033-0.12370.00740.1676-0.08010.0044-0.0099-0.00110.0913-0.01660.058125.749-16.017-20.121
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 45
2X-RAY DIFFRACTION2A46 - 84
3X-RAY DIFFRACTION3A85 - 102
4X-RAY DIFFRACTION4A103 - 175
5X-RAY DIFFRACTION5A176 - 203
6X-RAY DIFFRACTION6A204 - 220

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