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- PDB-5udg: Mutant E97Q crystal structure of Bacillus subtilis QueF with a di... -

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Basic information

Entry
Database: PDB / ID: 5udg
TitleMutant E97Q crystal structure of Bacillus subtilis QueF with a disulfide Cys 55-99
ComponentsNADPH-dependent 7-cyano-7-deazaguanine reductase
KeywordsOXIDOREDUCTASE / Tunnel fold / Disulfide inactivation / tRNA modification pathway / NADPH-dependent reduction of the nitrile group
Function / homology
Function and homology information


preQ1 synthase / preQ1 synthase activity / tRNA modification / tRNA queuosine(34) biosynthetic process / metal ion binding / cytoplasm / cytosol
Similarity search - Function
NADPH-dependent 7-cyano-7-deazaguanine reductase, QueF type 1 / NADPH-dependent 7-cyano-7-deazaguanine reductase QueF / : / QueF-like protein / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / NADPH-dependent 7-cyano-7-deazaguanine reductase / NADPH-dependent 7-cyano-7-deazaguanine reductase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMohammad, A. / Kiani, M.K. / Iwata-Reuyl, D. / Stec, B. / Swairjo, M.
CitationJournal: Biomolecules / Year: 2017
Title: Protection of the Queuosine Biosynthesis Enzyme QueF from Irreversible Oxidation by a Conserved Intramolecular Disulfide.
Authors: Mohammad, A. / Bon Ramos, A. / Lee, B.W. / Cohen, S.W. / Kiani, M.K. / Iwata-Reuyl, D. / Stec, B. / Swairjo, M.A.
History
DepositionDec 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH-dependent 7-cyano-7-deazaguanine reductase
B: NADPH-dependent 7-cyano-7-deazaguanine reductase
C: NADPH-dependent 7-cyano-7-deazaguanine reductase
D: NADPH-dependent 7-cyano-7-deazaguanine reductase
E: NADPH-dependent 7-cyano-7-deazaguanine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,00916
Polymers86,2385
Non-polymers77111
Water5,134285
1
A: NADPH-dependent 7-cyano-7-deazaguanine reductase
B: NADPH-dependent 7-cyano-7-deazaguanine reductase
C: NADPH-dependent 7-cyano-7-deazaguanine reductase
D: NADPH-dependent 7-cyano-7-deazaguanine reductase
E: NADPH-dependent 7-cyano-7-deazaguanine reductase
hetero molecules

A: NADPH-dependent 7-cyano-7-deazaguanine reductase
B: NADPH-dependent 7-cyano-7-deazaguanine reductase
C: NADPH-dependent 7-cyano-7-deazaguanine reductase
D: NADPH-dependent 7-cyano-7-deazaguanine reductase
E: NADPH-dependent 7-cyano-7-deazaguanine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,01732
Polymers172,47610
Non-polymers1,54222
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area44730 Å2
ΔGint-161 kcal/mol
Surface area49600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.308, 87.308, 196.734
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
NADPH-dependent 7-cyano-7-deazaguanine reductase / 7-cyano-7-carbaguanine reductase / NADPH-dependent nitrile oxidoreductase / PreQ(0) reductase


Mass: 17247.570 Da / Num. of mol.: 5 / Fragment: UNP resdiues 21-165 / Mutation: E97Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: queF, A9D36_18900, AX282_02560, B4122_4589, B4417_3799, BN2127_JRS11_03356, BN2127_JRS2_02117, BN2127_JRS6_01198, BN2127_JRS9_01727, SC09_Contig19orf00807
Production host: Escherichia coli (E. coli)
References: UniProt: A0A063X9I2, UniProt: O31678*PLUS, preQ1 synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 51 % / Description: Rhomboidal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein sample 4 mg/mL, in 50 mM Tris pH 7.5, 50 mM KCl, 1 mM MgCl2 and 1 mM (mercaptoethanol-BME) was mixed with reservoir solution (1:1 ratio) containing 19% PEG 550 monomethyl ether, 43 ...Details: Protein sample 4 mg/mL, in 50 mM Tris pH 7.5, 50 mM KCl, 1 mM MgCl2 and 1 mM (mercaptoethanol-BME) was mixed with reservoir solution (1:1 ratio) containing 19% PEG 550 monomethyl ether, 43 mM imidazole-Cl (pH 6.8), 53 mM imidazole (pH 8.2), 30 mM CaCl2, and 4% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→45.61 Å / Num. obs: 30298 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 14
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3 % / Rmerge(I) obs: 0.83 / CC1/2: 0.75 / % possible all: 89.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F8B

4f8b


Resolution: 2.5→45.61 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.89 / SU B: 12.067 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R: 0.723 / ESU R Free: 0.355 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29339 1516 5 %RANDOM
Rwork0.19428 ---
obs0.19906 28711 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.938 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20.91 Å20 Å2
2--1.81 Å20 Å2
3----2.72 Å2
Refinement stepCycle: 1 / Resolution: 2.5→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6065 0 44 285 6394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.026318
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9648544
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.345724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0924.114333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.641151059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1481530
X-RAY DIFFRACTIONr_chiral_restr0.1060.2847
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214957
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 96 -
Rwork0.268 1764 -
obs--88.83 %

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