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- PDB-4ig1: Crystal structure of Treponema pallidum TP0796 Flavin trafficking... -

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Basic information

Entry
Database: PDB / ID: 4ig1
TitleCrystal structure of Treponema pallidum TP0796 Flavin trafficking protein, Mg(II)-AMP product bound form
ComponentsFAD:protein FMN transferase
KeywordsHYDROLASE / bimetal center / FAD pyrophosphatase / flavin turnover / Treponema pallidum
Function / homology
Function and homology information


protein flavinylation / FAD:protein FMN transferase / membrane => GO:0016020 / transferase activity / metal ion binding / plasma membrane
Similarity search - Function
: / T-fold / ApbE-like domains / Flavin transferase ApbE / ApbE family / ApbE-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE MONOPHOSPHATE / FAD:protein FMN transferase / FAD:protein FMN transferase
Similarity search - Component
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4318 Å
AuthorsTomchick, D.R. / Brautigam, C.A. / Deka, R.K. / Norgard, M.V.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The TP0796 Lipoprotein of Treponema pallidum Is a Bimetal-dependent FAD Pyrophosphatase with a Potential Role in Flavin Homeostasis.
Authors: Deka, R.K. / Brautigam, C.A. / Liu, W.Z. / Tomchick, D.R. / Norgard, M.V.
History
DepositionDec 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Structure summary
Revision 1.2Mar 13, 2013Group: Database references
Revision 1.3May 8, 2013Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Feb 6, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_name_com / entity_src_gen / exptl_crystal_grow / software / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _exptl_crystal_grow.method / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.6Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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_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: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1985
Polymers36,7431
Non-polymers4554
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.998, 46.890, 57.471
Angle α, β, γ (deg.)90.00, 102.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-633-

HOH

21A-801-

HOH

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Components

#1: Protein FAD:protein FMN transferase / Flavin transferase


Mass: 36742.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum (strain Nichols) (bacteria)
Strain: Nichols / Gene: TPANIC_0796 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: R9UXK3, UniProt: O83774*PLUS, FAD:protein FMN transferase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 0.8 M sodium acetate, 0.1 M NaCl, 20% (w/v) ethylene glycol, pH 6.5, hanging-drop vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2012 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.43→50 Å / Num. all: 53906 / Num. obs: 53906 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.43-1.483.20.559196.7
1.48-1.53.40.5198.6
1.5-1.533.60.426199.9
1.53-1.563.70.3971100
1.56-1.63.90.3381100
1.6-1.633.90.2921100
1.63-1.673.90.2421100
1.67-1.723.90.2211100
1.72-1.773.90.191199.9
1.77-1.833.90.158199.7
1.83-1.893.90.132199.8
1.89-1.973.90.111199.5
1.97-2.063.90.097199.7
2.06-2.173.80.084199.7
2.17-2.33.80.074199.9
2.3-2.483.70.065199.9
2.48-2.733.70.057199.7
2.73-3.123.50.048199.5
3.12-3.943.50.041199.8
3.94-503.60.036196.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4IFU

4ifu


Resolution: 1.4318→28.558 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.14 / σ(F): 1.36 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2107 2731 5.07 %
Rwork0.1773 --
obs0.1789 53888 95.97 %
all-53481 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.5903 Å2
Refinement stepCycle: LAST / Resolution: 1.4318→28.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 0 29 256 2790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142681
X-RAY DIFFRACTIONf_angle_d1.283669
X-RAY DIFFRACTIONf_dihedral_angle_d12.104968
X-RAY DIFFRACTIONf_chiral_restr0.076419
X-RAY DIFFRACTIONf_plane_restr0.006480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4318-1.45650.3541430.298808X-RAY DIFFRACTION31
1.4565-1.4830.27761440.25732506X-RAY DIFFRACTION95
1.483-1.51150.29751520.23942637X-RAY DIFFRACTION99
1.5115-1.54240.2391370.21752631X-RAY DIFFRACTION100
1.5424-1.57590.2321660.20682645X-RAY DIFFRACTION100
1.5759-1.61260.22941280.2032681X-RAY DIFFRACTION100
1.6126-1.65290.2551480.19712617X-RAY DIFFRACTION100
1.6529-1.69760.24371460.18472639X-RAY DIFFRACTION100
1.6976-1.74750.231520.18472658X-RAY DIFFRACTION100
1.7475-1.80390.24061200.18732686X-RAY DIFFRACTION100
1.8039-1.86840.23211410.17982630X-RAY DIFFRACTION100
1.8684-1.94320.20541480.17692646X-RAY DIFFRACTION100
1.9432-2.03160.19381300.16442659X-RAY DIFFRACTION100
2.0316-2.13870.20311430.1682647X-RAY DIFFRACTION100
2.1387-2.27260.17581440.16082645X-RAY DIFFRACTION100
2.2726-2.4480.18841410.16032681X-RAY DIFFRACTION100
2.448-2.69420.18431510.16732652X-RAY DIFFRACTION100
2.6942-3.08360.20671220.17372706X-RAY DIFFRACTION99
3.0836-3.88350.2071390.17322709X-RAY DIFFRACTION100
3.8835-28.56340.21441360.17752674X-RAY DIFFRACTION96
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)
11.29830.4661-1.07660.8195-0.43771.90960.1124-0.16730.08680.2737-0.07510.0805-0.15180.1082-0.03120.20790.00790.07680.1695-0.01360.16441.791245.386217.1349
20.5476-0.1516-0.05941.5172-0.16820.5197-0.0018-0.014-0.03440.08130.01120.10770.0328-0.0190.02050.122-0.00060.05610.13820.00030.157838.500734.35479.2931
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 129 )
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 340 )

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