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- PDB-3i9s: Structure from the mobile metagenome of V.cholerae. Integron cass... -

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Basic information

Entry
Database: PDB / ID: 3i9s
TitleStructure from the mobile metagenome of V.cholerae. Integron cassette protein VCH_CASS6
ComponentsIntegron cassette protein
KeywordsTRANSFERASE / Integron cassette protein / Vibrio cholerae / Oyster pond / Woods hole / Acetyltransferase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyGcn5-related N-acetyltransferase (GNAT) / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsDeshpande, C.N. / Sureshan, V. / Harrop, S.J. / Boucher, Y. / Xu, X. / Cui, H. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Chang, C. ...Deshpande, C.N. / Sureshan, V. / Harrop, S.J. / Boucher, Y. / Xu, X. / Cui, H. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Chang, C. / Stokes, H.W. / Curmi, P.M.G. / Mabbutt, B.C. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure from the mobile metagenome of V.cholerae. Integron cassette protein VCH_CASS6
Authors: Deshpande, C.N. / Sureshan, V. / Harrop, S.J. / Boucher, Y. / G Curmi, P.M. / Stokes, H.W. / Edwards, A. / Savchenko, A. / Mabbutt, B.C.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 / 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.db_align_beg / _struct_ref_seq.db_align_end / _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: Integron cassette protein
B: Integron cassette protein
C: Integron cassette protein
D: Integron cassette protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,64616
Polymers83,7364
Non-polymers91012
Water5,819323
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19420 Å2
ΔGint-241 kcal/mol
Surface area29410 Å2
MethodPISA
2
A: Integron cassette protein
B: Integron cassette protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2277
Polymers41,8682
Non-polymers3595
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-103 kcal/mol
Surface area16470 Å2
MethodPISA
3
C: Integron cassette protein
D: Integron cassette protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4199
Polymers41,8682
Non-polymers5517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-127 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.239, 75.239, 310.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11C-165-

SO4

21B-213-

HOH

31C-219-

HOH

41C-312-

HOH

DetailsPossible dimer/tetramer.

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Components

#1: Protein
Integron cassette protein


Mass: 20933.939 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: OPVCH_OP3G / Gene: A59_A0465 / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 294 K / pH: 6.5
Details: 0.1M Bis-tris, 1.5M NH4SO4, In situ proteolysis using 1/1000chymotrypsin. Cryo: paratone-N oil, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2008
RadiationMonochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.2→52.44 Å / Num. all: 46726 / Num. obs: 46726 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.157 / Rsym value: 0.183 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.925 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6671 / Rsym value: 1.033 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.4_77)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→47.31 Å / SU ML: 0.34 / Isotropic thermal model: Isotropic / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 2152 4.62 %
Rwork0.183 --
obs0.185 46624 100 %
all-46624 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.9 Å2 / ksol: 0.35 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 44 323 5451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085229
X-RAY DIFFRACTIONf_angle_d0.9917026
X-RAY DIFFRACTIONf_dihedral_angle_d15.3251868
X-RAY DIFFRACTIONf_chiral_restr0.072761
X-RAY DIFFRACTIONf_plane_restr0.004882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25120.29131480.24212878X-RAY DIFFRACTION100
2.2512-2.30750.26931420.23132913X-RAY DIFFRACTION100
2.3075-2.36990.24351410.19712928X-RAY DIFFRACTION100
2.3699-2.43960.23151380.18442885X-RAY DIFFRACTION100
2.4396-2.51840.25181410.18232915X-RAY DIFFRACTION100
2.5184-2.60840.26141420.1842931X-RAY DIFFRACTION100
2.6084-2.71280.24571400.18742914X-RAY DIFFRACTION100
2.7128-2.83620.24031400.18582923X-RAY DIFFRACTION100
2.8362-2.98570.26111410.18772941X-RAY DIFFRACTION100
2.9857-3.17280.25771420.19492949X-RAY DIFFRACTION100
3.1728-3.41770.21681440.17282988X-RAY DIFFRACTION100
3.4177-3.76150.20471430.1582983X-RAY DIFFRACTION100
3.7615-4.30550.191450.13682994X-RAY DIFFRACTION100
4.3055-5.42320.19141480.14093077X-RAY DIFFRACTION100
5.4232-47.32520.23431570.20133253X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 42.9463 Å / Origin y: 0.1824 Å / Origin z: 134.6903 Å
111213212223313233
T0.2652 Å20.0042 Å2-0.1691 Å2-0.0357 Å20.0299 Å2--0.2747 Å2
L1.9896 °20.6608 °20.529 °2-0.9009 °2-0.1003 °2--1.3292 °2
S-0.282 Å °0.028 Å °0.5075 Å °-0.0826 Å °-0.0045 Å °0.2082 Å °-0.4021 Å °-0.048 Å °0.2873 Å °
Refinement TLS groupSelection details: CHAIN D

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