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- PDB-4fgc: Crystal Structure of Active Site Mutant C55A of Nitrile Reductase... -

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Basic information

Entry
Database: PDB / ID: 4fgc
TitleCrystal Structure of Active Site Mutant C55A of Nitrile Reductase QueF, Bound to Substrate PreQ0
ComponentsNADPH-dependent 7-cyano-7-deazaguanine reductase
KeywordsOXIDOREDUCTASE / beta barrel / pterin binding fold / tunnel fold / tRNA modification enzyme / 7-cyano-7-deazaguanine (PreQ0) binding / NADPH binding
Function / homology
Function and homology information


preQ1 synthase / preQ1 synthase activity / queuosine biosynthetic process / metal ion binding / cytoplasm
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-PQ0 / NADPH-dependent 7-cyano-7-deazaguanine reductase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.498 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
DepositionJun 4, 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_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_alt_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_seq_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_alt_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_ptnr1_label_alt_id / _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: 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)98,20018
Polymers96,8245
Non-polymers1,37613
Water3,693205
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)196,40036
Polymers193,64910
Non-polymers2,75126
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area44760 Å2
ΔGint-279 kcal/mol
Surface area48760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.048, 93.048, 193.651
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 / QueF / 7-cyano-7-carbaguanine reductase / NADPH-dependent nitrile oxidoreductase / PreQ(0) reductase


Mass: 19364.891 Da / Num. of mol.: 5 / Mutation: C55A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU13750, queF, ykvM / Plasmid: pET-30Xa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O31678, preQ1 synthase
#2: Chemical
ChemComp-PQ0 / 2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE / 7-DEAZA-7-CYANO-GUANINE


Mass: 175.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H5N5O
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7.4
Details: 16-20% PEG500 MME, 60 mM imidazole, 40 mM imidazolium chloride, pH 7.4, 30 mM calcium chloride, VAPOR DIFFUSION, 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: Feb 11, 2011 / 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: 2.498→22.151 Å / Num. all: 34498 / Num. obs: 31577 / % possible obs: 91.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 46.6 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.8
Reflection shellResolution: 2.498→2.54 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1498 / % possible all: 88.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4F8B

4f8b


Resolution: 2.498→22.15 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.86 / SU B: 14.033 / SU ML: 0.304 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.711 / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.30485 1592 5.1 %RANDOM
Rwork0.22836 ---
obs0.23225 29866 91.46 %-
all-34397 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.309 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.498→22.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6007 0 84 205 6296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226322
X-RAY DIFFRACTIONr_angle_refined_deg1.9971.9748561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3225723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.83324.067327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.073151044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4481529
X-RAY DIFFRACTIONr_chiral_restr0.0460.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214973
X-RAY DIFFRACTIONr_mcbond_it0.7441.53648
X-RAY DIFFRACTIONr_mcangle_it1.42425945
X-RAY DIFFRACTIONr_scbond_it1.85632674
X-RAY DIFFRACTIONr_scangle_it3.0334.52615
LS refinement shellResolution: 2.498→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 88 -
Rwork0.312 2087 -
obs--87.63 %

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