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- PDB-3rsb: Structure of the Archaeal GTP:AdoCbi-P Guanylyltransferase (CobY)... -

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Basic information

Entry
Database: PDB / ID: 3rsb
TitleStructure of the Archaeal GTP:AdoCbi-P Guanylyltransferase (CobY) from Methanocaldococcus jannaschii
ComponentsAdenosylcobinamide-phosphate guanylyltransferase
KeywordsTRANSFERASE / Pyrophosphorylase binding motif / pyrophosphorylase
Function / homology
Function and homology information


adenosylcobinamide-phosphate guanylyltransferase / cobinamide phosphate guanylyltransferase activity / cobalamin biosynthetic process / nucleotidyltransferase activity / GTP binding
Similarity search - Function
Conserved hypothetical protein CHP00454 / : / MobA-like NTP transferase / MobA-like NTP transferase domain / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Adenosylcobinamide-phosphate guanylyltransferase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsNewmister, S.A. / Otte, M.M. / Escalante-Semerena, J.C. / Rayment, I.
CitationJournal: Biochemistry / Year: 2011
Title: Structure and Mutational Analysis of the Archaeal GTP:AdoCbi-P Guanylyltransferase (CobY) from Methanocaldococcus jannaschii: Insights into GTP Binding and Dimerization.
Authors: Newmister, S.A. / Otte, M.M. / Escalante-Semerena, J.C. / Rayment, I.
History
DepositionMay 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_leaving_atom_flag / _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: Adenosylcobinamide-phosphate guanylyltransferase
B: Adenosylcobinamide-phosphate guanylyltransferase
C: Adenosylcobinamide-phosphate guanylyltransferase
D: Adenosylcobinamide-phosphate guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5328
Polymers88,4404
Non-polymers2,0934
Water2,702150
1
A: Adenosylcobinamide-phosphate guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6332
Polymers22,1101
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenosylcobinamide-phosphate guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6332
Polymers22,1101
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Adenosylcobinamide-phosphate guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6332
Polymers22,1101
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Adenosylcobinamide-phosphate guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6332
Polymers22,1101
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.600, 63.600, 222.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Adenosylcobinamide-phosphate guanylyltransferase / AdoCbi-P guanylyltransferase


Mass: 22109.893 Da / Num. of mol.: 4 / Mutation: G153D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: cobY, MJ1117 / Plasmid: pCobY14 / Production host: Escherichia coli (E. coli)
References: UniProt: Q58517, adenosylcobinamide-phosphate guanylyltransferase
#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
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: 2.94 Å3/Da / Density % sol: 58.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 60% 2-methyl-2,4-pentanediol, 0.1M 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: SBC-3 / Detector: CCD / Date: Nov 13, 2009 / Details: Mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.838
11-H, H+K, -L20.083
11K, H, -L30.079
ReflectionResolution: 2.8→50 Å / Num. all: 24528 / Num. obs: 24528 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 31.6
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 3.75 / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
SOLVEphasing
REFMAC5.5.0066refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→19.57 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.864 / SU B: 16.412 / SU ML: 0.33 / Cross valid method: THROUGHOUT / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27873 1098 4.8 %RANDOM
Rwork0.25587 ---
obs0.25695 21807 92.7 %-
all-21807 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5634 0 128 150 5912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0225875
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.3872.0297978
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3775713
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.92426.244213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.284151080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.639158
X-RAY DIFFRACTIONr_chiral_restr0.0240.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0214160
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.08923619
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.16235904
X-RAY DIFFRACTIONr_scbond_it0.10842256
X-RAY DIFFRACTIONr_scangle_it0.17962074
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 66 -
Rwork0.276 1329 -
obs--78.15 %

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