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- PDB-4f8b: Crystal Structure of the Covalent Thioimide Intermediate of Unimo... -

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Basic information

Entry
Database: PDB / ID: 4f8b
TitleCrystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase QueF
ComponentsNADPH-dependent 7-cyano-7-deazaguanine reductase
KeywordsOXIDOREDUCTASE / beta barrel / protein thioimide complex / pterin binding fold / tunnel fold / tRNA modification enzyme / 7-cyano-7-deazaguanine / NADPH
Function / homology
Function and homology information


preQ1 synthase / preQ1 synthase activity / tRNA modification / tRNA queuosine(34) biosynthetic process / metal ion binding / 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
Chem-GD1 / PHOSPHATE ION / NADPH-dependent 7-cyano-7-deazaguanine reductase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsStec, B. / Swairjo, M.A.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis of biological nitrile reduction.
Authors: Chikwana, V.M. / Stec, B. / Lee, B.W. / de Crecy-Lagard, V. / Iwata-Reuyl, D. / Swairjo, M.A.
History
DepositionMay 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Sep 19, 2012Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 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_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_label_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 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)98,24015
Polymers96,9855
Non-polymers1,25510
Water2,972165
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)196,48030
Polymers193,97010
Non-polymers2,51120
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area41190 Å2
ΔGint-187 kcal/mol
Surface area48840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.507, 93.507, 193.696
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 5 molecules ABCDE

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


Mass: 19396.955 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU13750, queF, ykvM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O31678, preQ1 synthase

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Non-polymers , 5 types, 175 molecules

#2: Chemical
ChemComp-GD1 / 2-amino-5-[(Z)-iminomethyl]-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one / 7-cyano-7-deazaguanine, bound form


Mass: 177.163 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H7N5O
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 16-20% PEG500 MME, 60 mM imidazole, 40 mM imidazolium chloride, pH 7.4, 30 mM calcium chloride or magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.000003 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2006 / Details: mirrors
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal, asymmetric cut 12.2 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000003 Å / Relative weight: 1
ReflectionResolution: 2.502→41.56 Å / Num. all: 34623 / Num. obs: 34623 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.9 % / Biso Wilson estimate: 54.7 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 7.8
Reflection shellResolution: 2.502→2.57 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.1 / % possible all: 89.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BP1

3bp1


Resolution: 2.502→41.56 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.886 / SU B: 9.355 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.445 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27195 1720 5 %RANDOM
Rwork0.18918 ---
obs0.19334 32475 98.72 %-
all-33897 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.536 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20.96 Å20 Å2
2--1.93 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.502→41.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6013 0 85 165 6263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0226292
X-RAY DIFFRACTIONr_angle_refined_deg2.0571.9778508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5335714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63924.08326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.63151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1211529
X-RAY DIFFRACTIONr_chiral_restr0.1290.2837
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024933
X-RAY DIFFRACTIONr_nbd_refined0.2510.22963
X-RAY DIFFRACTIONr_nbtor_refined0.3290.24190
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2309
X-RAY DIFFRACTIONr_metal_ion_refined0.2380.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.220
X-RAY DIFFRACTIONr_mcbond_it1.3391.53740
X-RAY DIFFRACTIONr_mcangle_it2.2125898
X-RAY DIFFRACTIONr_scbond_it2.92333031
X-RAY DIFFRACTIONr_scangle_it4.3484.52610
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 96 -
Rwork0.275 2153 -
obs--89.1 %

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