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- PDB-4u3q: Crystal Structure of Recombinant TP0435 from Treponema pallidum -

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Basic information

Entry
Database: PDB / ID: 4u3q
TitleCrystal Structure of Recombinant TP0435 from Treponema pallidum
Components17 kDa lipoprotein
KeywordsLIPID BINDING PROTEIN / lipoprotein / disulfide-linked dimer / beta barrel
Function / homologyLipocalin - #640 / Copper resistance lipoprotein NlpE / NlpE N-terminal domain / Lipocalin / Beta Barrel / Mainly Beta / plasma membrane / 17 kDa lipoprotein
Function and homology information
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBrautigam, C.A. / Deka, R.K. / Norgard, M.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI056305 United States
Citation
Journal: Protein Sci. / Year: 2015
Title: Insights into the potential function and membrane organization of the TP0435 (Tp17) lipoprotein from Treponema pallidum derived from structural and biophysical analyses.
Authors: Brautigam, C.A. / Deka, R.K. / Liu, W.Z. / Norgard, M.V.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Purification, crystallization and preliminary X-ray analysis of TP0435 (Tp17) from the syphilis spirochete Treponema pallidum.
Authors: Brautigam, C.A. / Deka, R.K. / Norgard, M.V.
History
DepositionJul 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 17 kDa lipoprotein
B: 17 kDa lipoprotein


Theoretical massNumber of molelcules
Total (without water)26,2462
Polymers26,2462
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-3 kcal/mol
Surface area11240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.682, 85.682, 85.376
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein 17 kDa lipoprotein


Mass: 13123.013 Da / Num. of mol.: 2 / Fragment: soluble domain (UNP residues 33-154)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum (bacteria) / Strain: Nichols / Gene: tpp17, TP_0435 / Plasmid: pE-SUMOpro / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29722
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 40% (v/v) PEG 400, 0.2 M lithium sulfate, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 9033 / % possible obs: 99.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 61.15 Å2 / Rmerge(I) obs: 0.048 / Χ2: 1.244 / Net I/av σ(I): 40.061 / Net I/σ(I): 14.9 / Num. measured all: 48918
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.4-2.444.20.5491.754190.71589.1
2.44-2.494.50.4544270.66896.4
2.49-2.534.80.4274400.68298.4
2.53-2.595.20.4014880.722100
2.59-2.645.50.3764280.693100
2.64-2.75.60.314710.776100
2.7-2.775.60.2144360.807100
2.77-2.855.60.1834830.864100
2.85-2.935.70.1324380.86100
2.93-3.025.70.1114680.904100
3.02-3.135.70.0924470.972100
3.13-3.265.70.0734540.99100
3.26-3.415.60.0594481.3100
3.41-3.585.70.054611.394100
3.58-3.815.60.0494581.663100
3.81-4.15.60.0454522.017100
4.1-4.525.50.0384462.185100
4.52-5.175.40.0364632.133100
5.17-6.515.50.0344482.048100
6.51-505.70.0314582.06299.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LHN

3lhn


Resolution: 2.4→37.002 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 33.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.275 896 9.93 %RANDOM
Rwork0.2307 8128 --
obs0.2352 9024 99.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.66 Å2 / Biso mean: 82.8921 Å2 / Biso min: 44.68 Å2
Refinement stepCycle: final / Resolution: 2.4→37.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1473 0 0 1 1474
Biso mean---44.68 -
Num. residues----192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031492
X-RAY DIFFRACTIONf_angle_d0.6541999
X-RAY DIFFRACTIONf_chiral_restr0.026232
X-RAY DIFFRACTIONf_plane_restr0.002246
X-RAY DIFFRACTIONf_dihedral_angle_d12.789556
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.55480.3761540.33311294144895
2.5548-2.7520.37891500.322713761526100
2.752-3.02880.32011530.272713681521100
3.0288-3.46680.29651580.263913451503100
3.4668-4.36670.2361390.209813731512100
4.3667-37.00620.25311420.200813721514100
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)
12.8133-0.5937-0.6445.307-2.78461.75160.15610.91510.1356-0.5814-0.18810.22330.3535-0.6498-0.06410.60270.04980.05320.78920.01190.6594-1.1298-16.7848-48.7545
22.9079-0.1162-1.62586.29122.22154.2680.2064-0.02390.41370.82850.1342-0.30910.5172-0.1043-0.33250.83240.02280.03010.52180.05950.60744.2345-16.9656-36.5455
32.01151.99646.93259.0692-7.19676.61171.27841.2196-3.09820.0096-1.7271.01821.82270.1404-0.45710.7515-0.11050.16250.9139-0.16462.009-10.018-24.6986-47.0367
47.489-1.12321.43596.4243-2.51628.7080.1173-0.8983-0.76940.8053-0.6724-0.48112.8437-0.66850.72840.87030.09150.18050.5717-0.04490.9495-0.6525-23.9974-37.135
52.0725-3.07572.5477.9048-5.5786.8104-0.0359-0.04340.02610.3995-0.64760.0595-0.0338-0.71240.16030.87240.05260.08620.70450.16580.5769-5.6398-20.2017-38.4225
66.44561.00553.35696.1172.03022.1273-1.74810.4271-0.7207-0.507-0.72330.49231.0952-0.98422.08940.666-0.02030.16420.61560.09750.9043-6.6644-12.2792-43.3398
71.0481-1.061.03413.96533.65298.57550.0169-0.0882-2.21240.0282-0.5704-0.32211.1883-1.76050.26370.5637-0.20180.18870.88710.21111.222-14.2313-14.8573-33.7908
89.6829-1.2664-4.1194.74971.07948.1094-0.98340.21690.4469-0.04520.39630.00270.3833-0.41090.98780.70830.0132-0.07270.54630.06550.6941-4.8366-7.3949-39.873
92.444-1.85740.6766.5913-0.73770.18750.2824-1.24010.60431.0857-0.030.84880.3014-0.6278-0.28120.8555-0.03540.10341.02360.10380.58486.5079-20.3942-59.6216
107.8763-0.78343.56257.331.37193.77150.069-0.1667-0.4108-0.2003-0.32310.72970.36120.02170.31580.52130.07570.07540.5712-0.0620.5759-2.2579-13.9708-74.9984
113.4632-0.73010.56663.09610.75.34280.50550.6832-2.535-0.3309-0.12271.89340.3875-0.20680.25660.75310.0622-0.00450.773-0.23131.5196-1.3157-22.3376-74.8931
128.26122.4434-4.55132.77561.57356.96070.4008-0.6171-1.8867-0.44840.04590.32491.17630.9457-0.22410.78380.12730.06640.46320.07241.0178.6953-23.3883-70.2085
133.9984-1.4124.04341.473-1.94545.6349-0.15530.0240.64030.5454-0.88650.86940.80590.41970.750.61080.11680.25370.7864-0.1960.76465.9716-19.3761-74.9862
146.03611.74680.025.75442.19062.3212-0.5182-0.32030.3471-0.1990.8439-0.1249-0.21960.3602-0.6360.70230.0278-0.03350.59090.02180.59657.9783-11.562-69.5107
154.79810.0144-0.3794.1550.37973.97590.0230.0390.6356-0.44740.22320.0738-0.2985-0.0577-0.22960.72440.0132-0.05230.5852-0.13970.626910.8807-9.4523-75.4461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 28 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 73 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 78 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 84 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 94 through 100 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 101 through 110 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 111 through 121 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 122 through 130 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 10 through 20 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 21 through 64 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 65 through 73 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 74 through 83 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 84 through 100 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 101 through 110 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 111 through 130 )B0

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