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- PDB-3pjn: The crystal structure of Tp34 bound to Zn(II) ion at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 3pjn
TitleThe crystal structure of Tp34 bound to Zn(II) ion at pH 7.5
Components34 kDa membrane antigen
KeywordsMEMBRANE PROTEIN / Ig fold / Metal binding / Human lactoferrin
Function / homology
Function and homology information


Periplasmic metal-binding protein Tp34-type / Periplasmic metal-binding protein Tp34-type / Periplasmic metal-binding protein Tp34-type superfamily / Fe2+ transport protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
34 kDa membrane antigen
Similarity search - Component
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsBrautigam, C.A. / Deka, R.K. / Tomchick, D.R. / Machius, M. / Norgard, M.V.
CitationJournal: To be Published
Title: Characterization of the Tp34 lipoprotein from Treponema pallidum suggests a role in transition metal homeostasis
Authors: Brautigam, C.A. / Deka, R.K. / Ouyang, Z. / Goldberg, M. / Machius, M. / Knutsen, G. / Tomchick, D.R. / Norgard, M.V.
History
DepositionNov 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: 34 kDa membrane antigen
B: 34 kDa membrane antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,97519
Polymers46,8352
Non-polymers1,13917
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-489 kcal/mol
Surface area14640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.573, 65.397, 152.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 34 kDa membrane antigen / Pathogen-specific membrane antigen


Mass: 23417.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum (bacteria) / Gene: tpd, TP_0971 / Production host: Escherichia coli (E. coli) / References: UniProt: P19478
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 1.84 Å3/Da / Density % sol: 33.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M Bicine, 2.4 M Ammonium Sulfate, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2008
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.7→32.9 Å / Num. all: 38964 / Num. obs: 38964 / % possible obs: 99.4 %
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.9 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→32.9 Å / SU ML: 0.18 / σ(F): 1.33 / Phase error: 19.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2061 1569 4.03 %
Rwork0.1782 --
obs0.1793 38888 99.66 %
all-38964 -
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.402 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.9574 Å2-0 Å2-0 Å2
2---2.7609 Å20 Å2
3----0.1965 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 24 200 2709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012610
X-RAY DIFFRACTIONf_angle_d1.3423552
X-RAY DIFFRACTIONf_dihedral_angle_d13.133930
X-RAY DIFFRACTIONf_chiral_restr0.103338
X-RAY DIFFRACTIONf_plane_restr0.006485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.75540.2931240.25443289X-RAY DIFFRACTION98
1.7554-1.81810.25761380.21663366X-RAY DIFFRACTION100
1.8181-1.89090.23971360.17883310X-RAY DIFFRACTION100
1.8909-1.97690.19821600.16533341X-RAY DIFFRACTION100
1.9769-2.08120.22371560.15453345X-RAY DIFFRACTION100
2.0812-2.21150.19861440.16753373X-RAY DIFFRACTION100
2.2115-2.38220.21741250.16773410X-RAY DIFFRACTION100
2.3822-2.62190.21591420.19013407X-RAY DIFFRACTION100
2.6219-3.0010.22181490.19123410X-RAY DIFFRACTION100
3.001-3.78010.19781360.17323478X-RAY DIFFRACTION100
3.7801-32.92010.18091590.17313590X-RAY DIFFRACTION99
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)
10.4640.26930.71841.18430.78421.28470.0126-0.03090.0262-0.09990.0221-0.0047-0.00710.014800.07690.005-0.01230.1522-0.03680.125810.85840.857962.0672
20.51210.59690.64821.39250.96331.08580.1483-0.0813-0.10790.12940.0271-0.05290.2133-0.02960.00090.2085-0.0003-0.08810.1072-0.01540.14546.621314.81352.7197
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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