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- PDB-3k8h: Structure of crystal form I of TP0453 -

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Basic information

Entry
Database: PDB / ID: 3k8h
TitleStructure of crystal form I of TP0453
Components30kLP
KeywordsMEMBRANE PROTEIN / Treponema pallidum / 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 / MOLECULAR REPLACEMENT / Resolution: 2.39 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 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: 30kLP
B: 30kLP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5314
Polymers58,2942
Non-polymers2362
Water2,324129
1
A: 30kLP
hetero molecules

B: 30kLP


Theoretical massNumber of molelcules
Total (without water)58,5314
Polymers58,2942
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1030 Å2
ΔGint-11 kcal/mol
Surface area25850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.297, 44.764, 96.965
Angle α, β, γ (deg.)90.00, 99.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 30kLP / Putative uncharacterized protein


Mass: 29147.111 Da / Num. of mol.: 2 / 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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.67 Å3/Da / Density % sol: 53.86 %
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, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 21, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. all: 24202 / Num. obs: 24202 / % possible obs: 98.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.6
Reflection shellResolution: 2.39→2.44 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 3.1 / % possible all: 82.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0088refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K8J

3k8j


Resolution: 2.39→42.72 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.904 / SU B: 16.239 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.401 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25804 1232 5.1 %RANDOM
Rwork0.20595 ---
obs0.20872 22964 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.426 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.21 Å2
2---0.03 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.39→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3967 0 16 129 4112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224073
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9645516
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9335498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39122.912182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.73515680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.161530
X-RAY DIFFRACTIONr_chiral_restr0.0840.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213072
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_it1.4161.52496
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5524033
X-RAY DIFFRACTIONr_scbond_it3.54331577
X-RAY DIFFRACTIONr_scangle_it5.5484.51483
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.454 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 72 -
Rwork0.245 1437 -
obs--81.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.88281.00060.62261.41440.08741.4997-0.03070.1702-0.0394-0.1170.07320.030.0009-0.0157-0.04250.07380.01080.01160.0487-0.01150.012821.5598-3.044834.3337
21.74-0.69550.51271.2583-1.04931.7374-0.0064-0.0082-0.0980.04740.05370.08220.0037-0.2538-0.04730.02170.00160.00970.0762-0.02980.066821.1104-19.0718-1.9866
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 282
2X-RAY DIFFRACTION2B31 - 282

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