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- PDB-3k8j: Structure of crystal form III of TP0453 -

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Basic information

Entry
Database: PDB / ID: 3k8j
TitleStructure of crystal form III of TP0453
Components30kLP
KeywordsMEMBRANE PROTEIN / Treponema pallidum / TP0453 / outer membrane protein
Function / homology: / Outer membrane-associated lipoprotein TP0453 / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Outer membrane protein TP0453
Function and homology information
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsZhu, G. / Luthra, A. / Desrosiers, D. / Koszelak-Rosenblum, M. / Mulay, V. / Radolf, J.D. / Malkowski, M.G.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The Transition from Closed to Open Conformation of Treponema pallidum Outer Membrane-associated Lipoprotein TP0453 Involves Membrane Sensing and Integration by Two Amphipathic Helices.
Authors: Luthra, A. / Zhu, G. / Desrosiers, D.C. / Eggers, C.H. / Mulay, V. / Anand, A. / McArthur, F.A. / Romano, F.B. / Caimano, M.J. / Heuck, A.P. / Malkowski, M.G. / Radolf, J.D.
History
DepositionOct 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 30kLP


Theoretical massNumber of molelcules
Total (without water)29,1471
Polymers29,1471
Non-polymers00
Water2,198122
1
A: 30kLP

A: 30kLP


Theoretical massNumber of molelcules
Total (without water)58,2942
Polymers58,2942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1060 Å2
ΔGint-14 kcal/mol
Surface area28480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.680, 157.508, 43.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 30kLP / Putative uncharacterized protein


Mass: 29147.111 Da / Num. of mol.: 1 / Fragment: residues 27-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum (bacteria) / Gene: 30klp, TP_0453 / Plasmid: pET43.1a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O67998
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 12% PEG 3350, 0.1M MgCl2, 0.1M MES, pH 5.5, 0.5% BOG, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-211
SYNCHROTRONSSRL BL9-220.97915,0.97932,0.96396
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDJun 13, 2009
MARMOSAIC 325 mm CCD2CCDMar 14, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979151
30.979321
40.963961
ReflectionResolution: 2.2→78.75 Å / Num. all: 16362 / Num. obs: 16362 / % possible obs: 98.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 43.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 6.8 / % possible all: 88.4

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Processing

Software
NameVersionClassification
Blu-Ice5data collection
SHARPphasing
REFMAC5.5.0088refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→78.75 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.902 / SU B: 10.001 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25972 827 5.1 %RANDOM
Rwork0.21157 ---
obs0.21394 15494 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.527 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2--2.2 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.2→78.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1971 0 0 122 2093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222046
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.9622775
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.265257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2722.82692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87715350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4641516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211553
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_it1.3631.51256
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34522036
X-RAY DIFFRACTIONr_scbond_it3.0463790
X-RAY DIFFRACTIONr_scangle_it4.7514.5735
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 59 -
Rwork0.187 1029 -
obs--90.74 %
Refinement TLS params.Method: refined / Origin x: 30.7385 Å / Origin y: 25.9564 Å / Origin z: 28.4194 Å
111213212223313233
T0.0325 Å20.0047 Å2-0.014 Å2-0.0354 Å2-0.0195 Å2--0.0239 Å2
L0.8356 °20.4961 °20.2217 °2-0.6211 °20.2351 °2--0.9833 °2
S0.0517 Å °-0.013 Å °-0.0664 Å °0.0342 Å °0.0039 Å °-0.0648 Å °0.1624 Å °-0.0144 Å °-0.0555 Å °

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