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- PDB-1toa: PERIPLASMIC ZINC BINDING PROTEIN TROA FROM TREPONEMA PALLIDUM -

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Basic information

Entry
Database: PDB / ID: 1toa
TitlePERIPLASMIC ZINC BINDING PROTEIN TROA FROM TREPONEMA PALLIDUM
ComponentsPROTEIN (PERIPLASMIC BINDING PROTEIN TROA)
KeywordsBINDING PROTEIN / PERIPLASMIC BINDING PROTEIN / ZINC BINDING PROTEIN / ABC TRANSPORTER
Function / homology
Function and homology information


zinc ion transport / periplasmic space / cell adhesion / metal ion binding
Similarity search - Function
Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Zinc-binding protein TroA
Similarity search - Component
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.8 Å
AuthorsLee, Y.H. / Deka, R.K. / Norgard, M.V. / Radolf, J.D. / Hasemann, C.A.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Treponema pallidum TroA is a periplasmic zinc-binding protein with a helical backbone.
Authors: Lee, Y.H. / Deka, R.K. / Norgard, M.V. / Radolf, J.D. / Hasemann, C.A.
History
DepositionMar 3, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 5, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: PROTEIN (PERIPLASMIC BINDING PROTEIN TROA)
B: PROTEIN (PERIPLASMIC BINDING PROTEIN TROA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2476
Polymers68,9322
Non-polymers3154
Water7,674426
1
A: PROTEIN (PERIPLASMIC BINDING PROTEIN TROA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6233
Polymers34,4661
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (PERIPLASMIC BINDING PROTEIN TROA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6233
Polymers34,4661
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.200, 126.200, 74.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Cell settinghexagonal
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.457452, 0.889145, 0.012599), (0.889042, 0.457013, 0.027281), (0.018499, 0.023681, -0.999548)
Vector: -0.5907, -0.6118, 71.1807)

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Components

#1: Protein PROTEIN (PERIPLASMIC BINDING PROTEIN TROA) / TROMP-1


Mass: 34465.883 Da / Num. of mol.: 2 / Fragment: SOLUBLE FRACTION
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH ZINC / Source: (gene. exp.) Treponema pallidum (bacteria) / Plasmid: PPROEX1 / Cell line (production host): DH5A / Production host: Escherichia coli (E. coli) / References: UniProt: P96116
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERM 27 AAS OF PROTEIN DERIVE FROM EXPRESSION VECTOR

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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: 2.77 Å3/Da / Density % sol: 55 %
Crystal growpH: 7 / Details: pH 7.0
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2LICL11
3PEG 400011
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.1 MNa-HEPES1reservoir
21.0 M1reservoirLiCl
330 %PEG40001reservoiror PEG6000

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1
DetectorType: ADSC / Detector: CCD / Date: Oct 15, 1998
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 62551 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 3.66 % / Biso Wilson estimate: 22.59 Å2 / Rsym value: 0.043 / Net I/σ(I): 38.9
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.37 % / Mean I/σ(I) obs: 4.25 / Rsym value: 0.28 / % possible all: 99.7
Reflection
*PLUS
Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.28

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.8→20 Å / Rfactor Rfree error: 0.0026 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.203 6102 10 %RANDOM
Rwork0.176 ---
obs-62551 99.889 %-
Displacement parametersBiso mean: 27.59 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4276 0 14 426 4716
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.382
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.23
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.750
X-RAY DIFFRACTIONx_mcangle_it2.730
X-RAY DIFFRACTIONx_scbond_it2.980
X-RAY DIFFRACTIONx_scangle_it4.640
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 1.8→1.88 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.274 771 9.89 %
Rwork0.278 7026 -
obs--100 %
Xplor fileSerial no: 1 / Param file: ENGH & HUBER / Topol file: ENGH & HUBER
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.23

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