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

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Basic information

Entry
Database: PDB / ID: 4ifu
TitleCrystal structure of Treponema pallidum TP0796 Flavin trafficking protein, apo 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
FAD:protein FMN transferase / FAD:protein FMN transferase
Similarity search - Component
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8334 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 1.4Feb 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_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_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 1.5Sep 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.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)36,7672
Polymers36,7431
Non-polymers241
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.587, 47.282, 57.593
Angle α, β, γ (deg.)90.00, 102.04, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-810-

HOH

21A-833-

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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: R9UXK3, UniProt: O83774*PLUS, FAD:protein FMN transferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate, 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: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2011 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. all: 27231 / Num. obs: 27231 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.83-1.863.90.574199.9
1.86-1.940.513198.9
1.9-1.9340.4651100
1.93-1.9740.341199.1
1.97-2.014.10.2781100
2.01-2.064.10.261199.6
2.06-2.114.10.221100
2.11-2.174.10.184199.7
2.17-2.234.10.1671100
2.23-2.314.10.138199.7
2.31-2.394.10.12199.7
2.39-2.4840.1081100
2.48-2.64.10.095199.9
2.6-2.7340.079199.9
2.73-2.940.0721100
2.9-3.133.90.061199.9
3.13-3.443.90.0511100
3.44-3.943.70.042199.9
3.94-4.973.80.0351100
4.97-503.80.034198.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VRM

1vrm


Resolution: 1.8334→28.75 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.19 / σ(F): 0 / Phase error: 21.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2171 1364 5.01 %
Rwork0.1693 --
obs0.1717 27219 99.41 %
all-27219 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.6911 Å2
Refinement stepCycle: LAST / Resolution: 1.8334→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2521 0 1 169 2691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182583
X-RAY DIFFRACTIONf_angle_d1.2773514
X-RAY DIFFRACTIONf_dihedral_angle_d12.354929
X-RAY DIFFRACTIONf_chiral_restr0.081402
X-RAY DIFFRACTIONf_plane_restr0.007461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8334-1.89890.26351290.21592446X-RAY DIFFRACTION96
1.8989-1.97490.24691210.20352630X-RAY DIFFRACTION99
1.9749-2.06480.23581470.18162558X-RAY DIFFRACTION100
2.0648-2.17360.22961460.17222555X-RAY DIFFRACTION100
2.1736-2.30970.22081110.16522616X-RAY DIFFRACTION100
2.3097-2.4880.21251430.16262603X-RAY DIFFRACTION100
2.488-2.73820.22841290.16982583X-RAY DIFFRACTION100
2.7382-3.1340.24821420.17822591X-RAY DIFFRACTION100
3.134-3.94690.2141530.16412606X-RAY DIFFRACTION100
3.9469-28.75370.18031430.15532667X-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)
10.03870.02320.0270.05910.03010.01440.0559-0.03940.02710.0282-0.09820.03110.03490.0316-0.00530.077-0.0072-0.01720.14860.01470.075153.971247.29-0.404
20.4293-0.19860.060.16290.00950.2632-0.01670.1010.16650.34-0.19070.0334-0.20860.0921-0.23280.2134-0.01440.0278-0.0247-0.11270.087543.173252.600117.4938
30.0226-0.0364-0.03140.20110.0790.04990.0263-0.10280.06110.18090.08640.1544-0.09340.02280.01070.20030.0020.04520.1622-0.01760.131334.111937.205325.2494
40.0503-0.0340.02590.0678-0.020.0053-0.12090.01040.0240.0830.07370.05570.0736-0.1581-0.08240.14950.02360.06030.11810.02120.127831.967948.912216.8821
50.03650.04790.04750.04260.01020.02320.04340.0177-0.0133-0.0121-0.03280.05570.06790.04840.00590.0706-0.0075-0.01280.079-0.01080.082247.957936.379-0.8621
60.0319-0.03820.0010.0749-0.02490.0348-0.0134-0.04430.0451-0.0554-0.03480.0116-0.06950.1404-0.01110.0748-0.0093-0.01610.12290.00320.089441.504628.050214.465
70.0441-0.0165-0.03530.0697-0.01050.05970.03580.0369-0.1209-0.0531-0.02830.1620.0093-0.02010.00110.10930.0117-0.01730.0856-0.01830.136736.003124.76134.3432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 76 )
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 131 )
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 179 )
5X-RAY DIFFRACTION5chain 'A' and (resid 180 through 225 )
6X-RAY DIFFRACTION6chain 'A' and (resid 226 through 279 )
7X-RAY DIFFRACTION7chain 'A' and (resid 280 through 340 )

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