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- PDB-3d37: The crystal structure of the tail protein from Neisseria meningit... -

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Basic information

Entry
Database: PDB / ID: 3d37
TitleThe crystal structure of the tail protein from Neisseria meningitidis MC58
ComponentsTail protein, 43 kDa
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / tail protein / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


: / : / Tail protein, C-terminal domain / Tail protein NMB1110-like, third domain / Baseplate protein-like domain - beta roll fold / Baseplate protein-like domains - 2 layer sandwich fold / Phage tail proteins - horseshoe like beta roll fold / Baseplate-like, two-layer sandwich fold / Baseplate protein GpP / : ...: / : / Tail protein, C-terminal domain / Tail protein NMB1110-like, third domain / Baseplate protein-like domain - beta roll fold / Baseplate protein-like domains - 2 layer sandwich fold / Phage tail proteins - horseshoe like beta roll fold / Baseplate-like, two-layer sandwich fold / Baseplate protein GpP / : / : / Mu phage baseplate assembly protein GpP-like, N-terminal / Baseplate hub protein gp44-like, second domain / Baseplate protein-like domains / Phage tail protein beta-alpha-beta fold / Phage tail proteins - 2 layer sandwich fold / 3-Layer(bab) Sandwich / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tail protein, 43 kDa
Similarity search - Component
Biological speciesNeisseria meningitidis MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsZhang, R. / Li, H. / Bargassa, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the tail protein from Neisseria meningitidis MC58.
Authors: Zhang, R. / Li, H. / Bargassa, M. / Joachimiak, A.
History
DepositionMay 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Tail protein, 43 kDa
B: Tail protein, 43 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4668
Polymers84,2542
Non-polymers2136
Water6,539363
1
A: Tail protein, 43 kDa
B: Tail protein, 43 kDa
hetero molecules

A: Tail protein, 43 kDa
B: Tail protein, 43 kDa
hetero molecules

A: Tail protein, 43 kDa
B: Tail protein, 43 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,39924
Polymers252,7616
Non-polymers63818
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area16230 Å2
ΔGint-19.2 kcal/mol
Surface area84570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.460, 137.460, 137.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Tail protein, 43 kDa


Mass: 42126.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Strain: MC58 / Serogroup B / Gene: GI:7226348, NMB1110 / Plasmid: pDM68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9JZC8
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M Potassium iodide, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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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 315 / Detector: CCD / Date: Dec 20, 2006 / Details: Mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→97.13 Å / Num. all: 48038 / Num. obs: 47918 / % possible obs: 99.75 % / Observed criterion σ(I): 2 / Redundancy: 28.5 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 38.89
Reflection shellResolution: 2.1→2.155 Å / Redundancy: 20.5 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.39 / Num. unique all: 3705 / % possible all: 99.57

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→97.13 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.241 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.214 / ESU R Free: 0.197
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27346 2563 5.1 %RANDOM
Rwork0.21952 ---
all0.22219 47918 --
obs0.22219 47918 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.105 Å2
Refinement stepCycle: LAST / Resolution: 2.1→97.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5029 0 6 363 5398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0225147
X-RAY DIFFRACTIONr_bond_other_d0.0020.023501
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.9476983
X-RAY DIFFRACTIONr_angle_other_deg1.0583.0018504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.395634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44223.652230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.16615860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4221537
X-RAY DIFFRACTIONr_chiral_restr0.1710.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025693
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021040
X-RAY DIFFRACTIONr_nbd_refined0.2330.21019
X-RAY DIFFRACTIONr_nbd_other0.2180.23618
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22269
X-RAY DIFFRACTIONr_nbtor_other0.0940.22799
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.2332
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3070.225
X-RAY DIFFRACTIONr_mcbond_it1.5321.54063
X-RAY DIFFRACTIONr_mcbond_other0.261.51307
X-RAY DIFFRACTIONr_mcangle_it1.78225120
X-RAY DIFFRACTIONr_scbond_it2.73832307
X-RAY DIFFRACTIONr_scangle_it3.9914.51863
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 173 -
Rwork0.277 3516 -
obs-3689 99.57 %
Refinement TLS params.Method: refined / Origin x: -22.636 Å / Origin y: 53.169 Å / Origin z: 97.926 Å
111213212223313233
T-0.0324 Å20.0024 Å20.0763 Å2--0.1136 Å2-0.0324 Å2---0.0225 Å2
L0.3187 °2-0.3357 °2-0.0558 °2-0.8535 °20.663 °2--0.9551 °2
S-0.0159 Å °0.0307 Å °0.0825 Å °-0.085 Å °-0.0261 Å °-0.0682 Å °-0.1915 Å °0.0099 Å °0.0421 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 3476 - 347
2X-RAY DIFFRACTION1BB6 - 3476 - 347

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