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- PDB-3pes: Crystal structure of uncharacterized protein from Pseudomonas pha... -

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Basic information

Entry
Database: PDB / ID: 3pes
TitleCrystal structure of uncharacterized protein from Pseudomonas phage YuA
ComponentsUncharacterized protein gp49
KeywordsStructural genomics / Unknown function / PSI2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyGMP Synthetase; Chain A, domain 3 - #260 / : / YuA phage, Gp49 / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / Structural phage protein
Function and homology information
Biological speciesPseudomonas phage YuA (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsNocek, B. / Stein, A. / Evdokimove, A. / Egorova, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of uncharacterized protein from Pseudomonas phage YuA
Authors: Nocek, B. / Stein, A. / Evdokimove, A. / Egorova, O. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionOct 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein gp49
B: Uncharacterized protein gp49


Theoretical massNumber of molelcules
Total (without water)19,7582
Polymers19,7582
Non-polymers00
Water5,513306
1
A: Uncharacterized protein gp49


Theoretical massNumber of molelcules
Total (without water)9,8791
Polymers9,8791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein gp49


Theoretical massNumber of molelcules
Total (without water)9,8791
Polymers9,8791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.059, 59.745, 38.154
Angle α, β, γ (deg.)90.00, 103.98, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Uncharacterized protein gp49


Mass: 9878.829 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage YuA (virus) / Gene: gp49 / Plasmid: pet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: A9J573
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.13 Å3/Da / Density % sol: 42.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M SPG, 25 % Peg3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.3→40 Å / Num. all: 40040 / Num. obs: 39941 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 29
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3893 / % possible all: 95.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXmodel building
ARP/wARPmodel building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→23.23 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.864 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.063 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20477 2015 5.1 %RANDOM
Rwork0.17553 ---
all0.18 39897 --
obs0.17708 37882 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.953 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.05 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.3→23.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1307 0 0 306 1613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221389
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.261.9611902
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6685173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.51421.64267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67815210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0051518
X-RAY DIFFRACTIONr_chiral_restr0.0750.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221114
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_it1.1031.5840
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8221354
X-RAY DIFFRACTIONr_scbond_it2.573549
X-RAY DIFFRACTIONr_scangle_it3.7234.5543
X-RAY DIFFRACTIONr_rigid_bond_restr1.16531389
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.297→1.331 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 155 -
Rwork0.228 2642 -
obs--91.83 %

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