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- PDB-1ypf: Crystal Structure of GuaC (BA5705) from Bacillus anthracis at 1.8... -

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Basic information

Entry
Database: PDB / ID: 1ypf
TitleCrystal Structure of GuaC (BA5705) from Bacillus anthracis at 1.8 A Resolution
ComponentsGMP reductase
KeywordsOXIDOREDUCTASE / GuaC / Purines / Pyrimidines / Nucleosides / Nucleotides / Nucleotide and nucleoside interconversions / SPINE / Structural Genomics / Structural Proteomics in Europe
Function / homology
Function and homology information


GMP reductase / GMP reductase complex / GMP reductase activity / purine nucleotide metabolic process / oxidoreductase activity, acting on the CH-CH group of donors / 'de novo' pyrimidine nucleobase biosynthetic process
Similarity search - Function
Guanosine monophosphate reductase, type2 / Dihydroorotate dehydrogenase, conserved site / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Guanosine monophosphate reductase, type2 / Dihydroorotate dehydrogenase, conserved site / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGrenha, R. / Levdikov, V.M. / Blagova, E.V. / Fogg, M.J. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S. / Structural Proteomics in Europe (SPINE)
CitationJournal: To be Published
Title: Crystal Structure of GuaC (BA5705) from Bacillus anthracis at 1.8 A Resolution.
Authors: Grenha, R. / Levdikov, V.M. / Blagova, E.V. / Fogg, M.J. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S.
History
DepositionJan 31, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 20, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GMP reductase
B: GMP reductase


Theoretical massNumber of molelcules
Total (without water)74,3672
Polymers74,3672
Non-polymers00
Water12,286682
1
A: GMP reductase

A: GMP reductase

A: GMP reductase

A: GMP reductase


Theoretical massNumber of molelcules
Total (without water)148,7334
Polymers148,7334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area9740 Å2
ΔGint-48 kcal/mol
Surface area47670 Å2
MethodPISA, PQS
2
B: GMP reductase


Theoretical massNumber of molelcules
Total (without water)37,1831
Polymers37,1831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: GMP reductase

B: GMP reductase

B: GMP reductase

B: GMP reductase


Theoretical massNumber of molelcules
Total (without water)148,7334
Polymers148,7334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)114.676, 114.676, 52.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein GMP reductase / / Guanosine monophosphate reductase / Guanosine 5'-monophosphate oxidoreductase


Mass: 37183.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: guaC / Plasmid: pET-YSBLIC / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q81JJ9, GMP reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 682 / 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: 2.4 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPD, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 2004 / Details: Rh coated Si mirror
RadiationMonochromator: Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 63577 / Num. obs: 63577 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 17.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 1.6 / Num. unique all: 6280 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JR1

1jr1


Resolution: 1.8→29.85 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.453 / SU ML: 0.102 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.204 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23778 3224 5.1 %RANDOM
Rwork0.1744 ---
all0.17758 60333 --
obs0.17758 60333 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.971 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å20 Å2
2---1.34 Å20 Å2
3---2.67 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4547 0 0 682 5229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224660
X-RAY DIFFRACTIONr_bond_other_d0.0020.024268
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9536297
X-RAY DIFFRACTIONr_angle_other_deg1.06539968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4395596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89824.826201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12415834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3581522
X-RAY DIFFRACTIONr_chiral_restr0.1530.2716
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025180
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02890
X-RAY DIFFRACTIONr_nbd_refined0.2180.21005
X-RAY DIFFRACTIONr_nbd_other0.1920.24309
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22205
X-RAY DIFFRACTIONr_nbtor_other0.0850.22599
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2477
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.040.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1423834
X-RAY DIFFRACTIONr_mcbond_other0.70921224
X-RAY DIFFRACTIONr_mcangle_it2.7644744
X-RAY DIFFRACTIONr_scbond_it4.1961974
X-RAY DIFFRACTIONr_scangle_it5.553101549
X-RAY DIFFRACTIONr_rigid_bond_restr2.343310612
X-RAY DIFFRACTIONr_sphericity_free5.6893689
X-RAY DIFFRACTIONr_sphericity_bonded2.79238844
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 228 -
Rwork0.252 4411 -
obs-4411 100 %

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