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- PDB-3bp1: Crystal structure of putative 7-cyano-7-deazaguanine reductase Qu... -

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Basic information

Entry
Database: PDB / ID: 3bp1
TitleCrystal structure of putative 7-cyano-7-deazaguanine reductase QueF from Vibrio cholerae O1 biovar eltor
ComponentsNADPH-dependent 7-cyano-7-deazaguanine reductase
KeywordsOXIDOREDUCTASE / alpha-beta structure / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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
GUANINE / PHOSPHATE ION / PYROPHOSPHATE 2- / : / NADPH-dependent 7-cyano-7-deazaguanine reductase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar eltor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.53 Å
AuthorsKim, Y. / Zhou, M. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: High-resolution structure of the nitrile reductase QueF combined with molecular simulations provide insight into enzyme mechanism.
Authors: Kim, Y. / Zhou, M. / Moy, S. / Morales, J. / Cunningham, M.A. / Joachimiak, A.
History
DepositionDec 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 17, 2012Group: Database references
Remark 999 SEQUENCE THE CLOSEST SEQUENCE MATCH FOR THIS ENTRY IS AN UNIPROT ENTRY A6Y463_VIBCH, OF THE VIBRIO ... SEQUENCE THE CLOSEST SEQUENCE MATCH FOR THIS ENTRY IS AN UNIPROT ENTRY A6Y463_VIBCH, OF THE VIBRIO CHOLERAE RC385 STRAIN. AUTHORS STATE THAT THE SOURCE OF THEIR PROTEIN IS VIBRIO CHOLERAE O1 BIOVAR ELTOR STRAIN N16961, NCBI ACCESSION AAF94064, GI:9655358.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)134,83618
Polymers133,2614
Non-polymers1,57514
Water21,2041177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)67,4189
Polymers66,6312
Non-polymers7877
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
MethodPISA
3
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)67,4189
Polymers66,6312
Non-polymers7877
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.517, 71.578, 71.511
Angle α, β, γ (deg.)119.25, 110.18, 99.58
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 33315.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar eltor str. N16961 (bacteria)
Species: Vibrio cholerae / Strain: El Tor Inaba N16961 / Serotype O1 / Gene: queF, VC_0902 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A6Y463, UniProt: Q9KTK0*PLUS, preQ1 synthase

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Non-polymers , 5 types, 1191 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5O
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1177 / 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: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.04M Sodium dihydrogen phosphate, 0.96M Di-potassium hydrogen phosphate, GTP, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 29, 2007 / Details: Mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. all: 149957 / Num. obs: 149957 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rsym value: 0.069 / Net I/σ(I): 7.5
Reflection shellResolution: 1.53→1.58 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 12259 / Rsym value: 0.359 / % possible all: 76.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXphasing
MLPHAREphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.53→26.16 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.773 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.079
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: Program PHENIX has also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.183 7527 5 %RANDOM
Rwork0.143 ---
all0.145 142270 --
obs0.145 142270 93.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.199 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0.18 Å2-0.29 Å2
2--0.89 Å21.12 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.53→26.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8197 0 94 1177 9468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0219589
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.94813200
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1351238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.44824.981526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.391151604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0711565
X-RAY DIFFRACTIONr_chiral_restr0.1120.21377
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027849
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.24890
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.26690
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.21166
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1240.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.2102
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.521.55974
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.28929543
X-RAY DIFFRACTIONr_scbond_it3.20834128
X-RAY DIFFRACTIONr_scangle_it4.3934.53657
X-RAY DIFFRACTIONr_rigid_bond_restr1.995310102
X-RAY DIFFRACTIONr_sphericity_free6.27431179
X-RAY DIFFRACTIONr_sphericity_bonded4.44639300
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 396 -
Rwork0.178 7702 -
obs-1198 68.98 %

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