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- PDB-2r9i: Crystal structure of putative phage capsid protein domain from Co... -

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Basic information

Entry
Database: PDB / ID: 2r9i
TitleCrystal structure of putative phage capsid protein domain from Corynebacterium diphtheriae
ComponentsPutative phage capsid protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Putative phage capsid domain / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyDIP0205-like, N-terminal domain / Phage capsid / Phage capsid family / ATP synthase, gamma subunit, helix hairpin domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Phage capsid protein
Function and homology information
Biological speciesCorynebacterium diphtheriae NCTC 13129 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsWu, R. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of putative phage capsid protein domain from Corynebacterium diphtheriae.
Authors: Wu, R. / Abdullah, J. / Joachimiak, A.
History
DepositionSep 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 16, 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: Putative phage capsid protein


Theoretical massNumber of molelcules
Total (without water)15,5211
Polymers15,5211
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.905, 102.905, 102.905
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Putative phage capsid protein


Mass: 15520.618 Da / Num. of mol.: 1 / Fragment: N-terminal domain: Residues 1-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae NCTC 13129 (bacteria)
Species: Corynebacterium diphtheriae / Strain: NCTC 13129 / Biotype gravis / Gene: DIP0205 / Plasmid: pDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6NK34
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-tris propane pH 7.0, 3.5M Sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9798 Å
DetectorType: SBC-2 / Detector: CCD / Date: Aug 19, 2007 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 5692 / Num. obs: 5692 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 20.4 % / Biso Wilson estimate: 80.16 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 46.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 21.1 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→32.55 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.952 / SU B: 15.927 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.204
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Residues 73-138 are missing in coordinates due to lack of electron density
RfactorNum. reflection% reflectionSelection details
Rfree0.24184 258 4.5 %RANDOM
Rwork0.21858 ---
obs0.21967 5416 99.58 %-
all-5416 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.252 Å2
Refinement stepCycle: LAST / Resolution: 2.6→32.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms543 0 0 9 552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022543
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.971730
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.173571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.71225.625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.85615106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.106155
X-RAY DIFFRACTIONr_chiral_restr0.1860.289
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02395
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2540.2236
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.2376
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.217
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7491.5364
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4542573
X-RAY DIFFRACTIONr_scbond_it2.4093187
X-RAY DIFFRACTIONr_scangle_it4.464.5157
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.508 16 -
Rwork0.326 392 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 27.9599 Å / Origin y: 48.9035 Å / Origin z: 6.9054 Å
111213212223313233
T-0.1899 Å2-0.0809 Å2-0.0846 Å2--0.1314 Å20.1242 Å2---0.0418 Å2
L7.2477 °21.8517 °2-4.6434 °2-3.4274 °2-1.2359 °2--3.4009 °2
S-0.1502 Å °-0.3391 Å °-0.4219 Å °0.5426 Å °-0.4908 Å °-0.5433 Å °-0.0364 Å °0.1053 Å °0.641 Å °

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