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- PDB-3s19: Crystal Structure of the R262L mutant of 7-cyano-7-deazaguanine r... -

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Basic information

Entry
Database: PDB / ID: 3s19
TitleCrystal Structure of the R262L mutant of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with preQ0
ComponentsNADPH-dependent 7-cyano-7-deazaguanine reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta structure / tunneling fold / reductase / cytosol
Function / homology
Function and homology information


preQ1 synthase / preQ1 synthase activity / queuosine biosynthetic process / cytoplasm
Similarity search - Function
NADPH-dependent 7-cyano-7-deazaguanine reductase, QueF type 2 / NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal / Nitrile reductase, 7-cyano-7-deazaguanine-reductase N-term / 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
7-DEAZA-7-AMINOMETHYL-GUANINE / NADPH-dependent 7-cyano-7-deazaguanine reductase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5009 Å
AuthorsKim, Y. / Zhou, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of the R262L mutant of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with preQ0
Authors: Kim, Y. / Zhou, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / CSGID
History
DepositionMay 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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_conn.ptnr2_label_seq_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 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,17012
Polymers133,0854
Non-polymers1,0858
Water21,4741192
1
A: NADPH-dependent 7-cyano-7-deazaguanine reductase
B: NADPH-dependent 7-cyano-7-deazaguanine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0856
Polymers66,5432
Non-polymers5434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-7 kcal/mol
Surface area20440 Å2
MethodPISA
2
C: NADPH-dependent 7-cyano-7-deazaguanine reductase
D: NADPH-dependent 7-cyano-7-deazaguanine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0856
Polymers66,5432
Non-polymers5434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-5 kcal/mol
Surface area20190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.326, 71.330, 71.328
Angle α, β, γ (deg.)109.98, 119.51, 99.50
Int Tables number1
Space group name H-MP1

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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: 33271.285 Da / Num. of mol.: 4 / Mutation: R256L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: N16961 / Gene: queF, VC_0902 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9KTK0, preQ1 synthase
#2: Chemical
ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H9N5O
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1192 / 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: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Citrate pH 5.5, 20 % PEG3000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 155040 / Num. obs: 155040 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 13.32 Å2 / Rsym value: 0.03 / Net I/σ(I): 20
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 7.8 / Num. unique all: 4801 / Rsym value: 0.11 / % possible all: 57.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_725)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 3BP1

3bp1


Resolution: 1.5009→30.979 Å / SU ML: 0.35 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.176 7763 5.01 %random
Rwork0.152 ---
all0.153 155035 --
obs0.153 155035 92.35 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.967 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso mean: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.064 Å2-1.3741 Å21.4786 Å2
2---2.0978 Å2-3.1062 Å2
3---3.1618 Å2
Refinement stepCycle: LAST / Resolution: 1.5009→30.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8342 0 76 1192 9610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810055
X-RAY DIFFRACTIONf_angle_d1.44313889
X-RAY DIFFRACTIONf_dihedral_angle_d15.8193810
X-RAY DIFFRACTIONf_chiral_restr0.1051460
X-RAY DIFFRACTIONf_plane_restr0.011930
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.5009-1.5180.21431380.18312964311254
1.518-1.53580.19551590.19853221338062
1.5358-1.55460.21781830.19073696387968
1.5546-1.57420.23762100.18354107431778
1.5742-1.5950.20562640.15994948521293
1.595-1.61680.1922590.16575046530595
1.6168-1.63990.16912580.16655037529595
1.6399-1.66440.21142840.15755061534596
1.6644-1.69040.18272670.15555076534396
1.6904-1.71810.17912700.15695068533896
1.7181-1.74770.18552880.14225143543196
1.7477-1.77950.17132860.14035114540096
1.7795-1.81370.17533030.14664988529196
1.8137-1.85070.1852950.15085074536996
1.8507-1.8910.18142750.15555174544996
1.891-1.9350.18182770.14485164544197
1.935-1.98330.16182760.14195180545697
1.9833-2.0370.1882760.14855093546997
2.037-2.09690.19152590.15495220547997
2.0969-2.16450.17922330.15375159539297
2.1645-2.24190.18132810.15185130541197
2.2419-2.33160.1732730.1515165543898
2.3316-2.43770.17982940.14885213550798
2.4377-2.56620.18332710.16185230550198
2.5662-2.72680.17852400.15515213545398
2.7268-2.93720.18452870.15895174546198
2.9372-3.23250.19262580.15525289554798
3.2325-3.69960.15752680.13515221548999
3.6996-4.65860.1352590.12775203546298
4.6586-30.98560.17932720.16964901517392
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)
10.75410.0275-0.26822.70592.52173.8058-0.10590.0543-0.0786-0.0766-0.24640.3556-0.0463-0.44890.1450.1316-0.03650.02140.1437-0.00630.1358-22.9464-31.769610.1265
20.59020.0377-0.07710.71120.27091.04510.03710.0271-0.1813-0.0561-0.0483-0.05330.104-0.11310.0210.1166-0.01750.00620.0770.01810.1125-12.59-30.96956.3977
30.32480.191-0.20910.74650.2550.654-0.043-0.0044-0.0930.11640.0059-0.01740.14950.02630.02650.11310.00610.00410.08760.02390.0816-10.3465-24.934213.8302
41.26930.23710.59840.4878-0.05421.4072-0.09380.1306-0.0838-0.14450.0460.00330.03140.06990.03930.1813-0.01410.00580.1246-0.01910.1089-11.4051-24.0089-19.8317
50.38780.16420.28680.4434-0.30370.6950.01140.1799-0.1904-0.1109-0.04490.0510.1457-0.0963-0.00220.132-0.01810.00870.1344-0.04630.1233-12.938-31.5882-15.8691
60.8322-0.7310.14542.03950.391.2515-0.05820.0246-0.04280.07240.0667-0.00950.1624-0.02640.04350.0868-0.00920.01170.08430.00180.0984-10.5249-28.6831-11.8377
70.4965-0.0390.10061.2252-0.19541.87180.00750.0605-0.1253-0.0843-0.04320.10380.1669-0.04990.00940.1164-0.02630.00370.1131-0.020.1103-15.2972-34.0566-14.2787
80.4633-0.3529-0.00741.64240.72650.8597-0.02420.0182-0.08560.05860.0203-0.10530.09020.04920.0060.10360.00310.0130.09380.00020.0945-7.3323-29.1828-4.178
90.6487-0.1583-0.02940.72040.17620.57150.01840.0310.0533-0.0715-0.04550.077-0.0436-0.10050.03080.0630.0059-0.01390.08260.00260.0611-19.9108-2.4252-7.5863
100.43020.14110.08110.57670.36160.68470.0143-0.08170.01810.0251-0.03020.0473-0.041-0.02330.00890.06-0.0103-0.00230.06150.00620.0376-12.74561.394714.0318
110.6671-0.2025-0.07930.81630.06170.58430.02420.09780.0157-0.1744-0.0208-0.084-0.0143-0.00270.02020.09150.00180.00690.05830.02080.0418.515811.1805-18.4163
120.3818-0.0389-0.09760.42620.12840.36420.0070.03450.0056-0.0476-0.0184-0.012-0.0628-0.01910.00620.0790.00070.00180.07530.00680.07556.86711.2939-8.987
130.3909-0.0508-0.09451.02020.12310.3223-0.00370.0235-0.0558-0.0935-0.0138-0.0521-0.00470.03390.02350.06670.0052-0.00590.06250.01010.084315.209-3.8299-9.8601
141.1546-0.8482-0.2292.68790.58280.71220.14380.04890.2121-0.3064-0.0223-0.1857-0.11540.0983-0.00470.0947-0.02530.02410.1171-0.00970.190732.012524.31244.7896
150.8074-0.3403-0.13011.1320.13470.5740.0519-0.09430.14720.0798-0.0543-0.1051-0.13120.0027-0.08280.0873-0.0098-0.01990.1063-0.01520.118124.31219.550510.778
160.5255-0.0729-0.14341.12520.50980.29360.0048-0.07150.0720.06640.0634-0.1250.01310.0716-0.05650.06840.0071-0.01760.1232-0.01430.107729.433912.00468.6917
171.58130.25540.46010.06320.06490.3404-0.0067-0.20980.0540.0792-0.00180.0546-0.04810.0025-0.03660.11980.0019-0.00840.13140.01050.09517.71469.391813.1832
180.9525-0.32290.07951.2786-0.60670.9180.0117-0.07190.14070.04540.0340.1997-0.1065-0.0531-0.06920.12240.0138-0.00360.1018-0.01750.16891.076132.03594.9481
191.08770.06150.1680.5479-0.3580.27390.0360.0120.18280.0093-0.0305-0.034-0.15270.00120.00420.1177-0.00040.01760.080.00020.138110.41734.46585.8467
200.4943-0.1944-0.14450.77510.49541.1450.0105-0.07420.11430.10990.0592-0.0412-0.0280.0527-0.02780.0973-0.00450.01320.1048-0.01780.09457.441230.501110.4844
211.2627-0.54360.49761.27130.2080.8673-0.0071-0.02840.1937-0.05250.0067-0.1021-0.18480.0416-0.00110.1131-0.00850.0160.0879-0.00350.156911.16937.24738.431
220.8841-0.6696-0.57281.98251.40792.07630.0612-0.07220.10440.05490.0471-0.1516-0.05740.0612-0.08250.0838-0.00210.00660.0902-0.00910.094814.17626.688411.0872
230.38780.58420.50981.25510.63080.72060.0635-0.20790.04060.27-0.11470.10220.1552-0.10830.00170.14470.0040.01210.1702-0.01390.113310.749120.514315.2296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 27:47)
2X-RAY DIFFRACTION2chain 'A' and (resseq 48:75)
3X-RAY DIFFRACTION3chain 'A' and (resseq 76:147)
4X-RAY DIFFRACTION4chain 'A' and (resseq 148:167)
5X-RAY DIFFRACTION5chain 'A' and (resseq 168:198)
6X-RAY DIFFRACTION6chain 'A' and (resseq 199:212)
7X-RAY DIFFRACTION7chain 'A' and (resseq 213:248)
8X-RAY DIFFRACTION8chain 'A' and (resseq 249:287)
9X-RAY DIFFRACTION9chain 'B' and (resseq 29:147)
10X-RAY DIFFRACTION10chain 'B' and (resseq 148:287)
11X-RAY DIFFRACTION11chain 'C' and (resseq 29:75)
12X-RAY DIFFRACTION12chain 'C' and (resseq 76:167)
13X-RAY DIFFRACTION13chain 'C' and (resseq 168:287)
14X-RAY DIFFRACTION14chain 'D' and (resseq 27:48)
15X-RAY DIFFRACTION15chain 'D' and (resseq 49:75)
16X-RAY DIFFRACTION16chain 'D' and (resseq 76:128)
17X-RAY DIFFRACTION17chain 'D' and (resseq 129:147)
18X-RAY DIFFRACTION18chain 'D' and (resseq 148:167)
19X-RAY DIFFRACTION19chain 'D' and (resseq 168:199)
20X-RAY DIFFRACTION20chain 'D' and (resseq 200:212)
21X-RAY DIFFRACTION21chain 'D' and (resseq 213:248)
22X-RAY DIFFRACTION22chain 'D' and (resseq 249:272)
23X-RAY DIFFRACTION23chain 'D' and (resseq 273:287)

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