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- PDB-4njj: Crystal Structure of QueE from Burkholderia multivorans in comple... -

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Basic information

Entry
Database: PDB / ID: 4njj
TitleCrystal Structure of QueE from Burkholderia multivorans in complex with AdoMet, 6-carboxy-5,6,7,8-tetrahydropterin, and Manganese(II)
Components7-carboxy-7-deazaguanine synthase
KeywordsLYASE / AdoMet radical enzyme / modified partial TIM barrel-like structure / radical SAM fold / radical AdoMet fold / synthase
Function / homology
Function and homology information


7-carboxy-7-deazaguanine synthase / carbon-nitrogen lyase activity / tRNA queuosine(34) biosynthetic process / S-adenosyl-L-methionine binding / 4 iron, 4 sulfur cluster binding / magnesium ion binding / protein homodimerization activity / identical protein binding
Similarity search - Function
7-carboxy-7-deazaguanine synthase, Cx14CxxC-type / 7-carboxy-7-deazaguanine synthase-like / : / Radical SAM core domain profile. / Radical SAM / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-2K8 / : / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / 7-carboxy-7-deazaguanine synthase / 7-carboxy-7-deazaguanine synthase
Similarity search - Component
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDowling, D.P. / Bruender, N.A. / Young, A.P. / McCarty, R.M. / Bandarian, V. / Drennan, C.L.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism.
Authors: Dowling, D.P. / Bruender, N.A. / Young, A.P. / McCarty, R.M. / Bandarian, V. / Drennan, C.L.
History
DepositionNov 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Jul 2, 2014Group: Non-polymer description
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_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: 7-carboxy-7-deazaguanine synthase
B: 7-carboxy-7-deazaguanine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,83012
Polymers50,6872
Non-polymers2,14210
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-79 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.174, 119.174, 105.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 7-carboxy-7-deazaguanine synthase / CDG synthase / Queuosine biosynthesis protein QueE


Mass: 25343.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (bacteria) / Strain: ATCC 17616 / 249 / Gene: queE, Bmul_3115, BMULJ_00116 / Production host: Escherichia coli (E. coli)
References: UniProt: A9AC61, UniProt: A0A0H3KB22*PLUS, 7-carboxy-7-deazaguanine synthase

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Non-polymers , 5 types, 79 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-2K8 / (6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridine-6-carboxylic acid / 6-carboxy-5,6,7,8-tetrahydropterin


Mass: 211.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9N5O3
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.69 Å3/Da / Density % sol: 66.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: anaerobic, crystals formed in 2.0 M sodium dipotassium phosphate, pH 6.8, 0.1 M sodium acetate, pH 4.5, buffer-exchanged into 0.1 M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, 0.1 M manganese ...Details: anaerobic, crystals formed in 2.0 M sodium dipotassium phosphate, pH 6.8, 0.1 M sodium acetate, pH 4.5, buffer-exchanged into 0.1 M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, 0.1 M manganese sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.7399 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 13, 2012
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7399 Å / Relative weight: 1
ReflectionResolution: 2.7→48.2 Å / Num. obs: 21371 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 63.2 Å2 / Rsym value: 0.076 / Net I/σ(I): 27.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.551 / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NJG

4njg


Resolution: 2.7→48.163 Å / SU ML: 0.3 / σ(F): 1.36 / Phase error: 21.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 1048 5.06 %
Rwork0.1607 --
obs0.1626 21361 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→48.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 104 69 3413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043452
X-RAY DIFFRACTIONf_angle_d0.7734720
X-RAY DIFFRACTIONf_dihedral_angle_d11.5071296
X-RAY DIFFRACTIONf_chiral_restr0.027500
X-RAY DIFFRACTIONf_plane_restr0.004656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6998-2.76730.35521420.26332662X-RAY DIFFRACTION99
2.7673-2.84210.2581700.21772677X-RAY DIFFRACTION100
2.8421-2.92570.22851240.19572700X-RAY DIFFRACTION100
2.9257-3.02010.26151290.19612703X-RAY DIFFRACTION100
3.0201-3.12810.23711710.20942680X-RAY DIFFRACTION100
3.1281-3.25330.27791200.20652734X-RAY DIFFRACTION100
3.2533-3.40130.25671370.19512691X-RAY DIFFRACTION100
3.4013-3.58060.21251620.18452669X-RAY DIFFRACTION100
3.5806-3.80480.25431540.18242702X-RAY DIFFRACTION100
3.8048-4.09850.17411430.15092704X-RAY DIFFRACTION100
4.0985-4.51060.17551460.12672673X-RAY DIFFRACTION100
4.5106-5.16270.15071380.12642706X-RAY DIFFRACTION100
5.1627-6.50190.15121250.13862736X-RAY DIFFRACTION100
6.5019-48.1710.16991470.13792620X-RAY DIFFRACTION97

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