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

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Basic information

Entry
Database: PDB / ID: 4ifw
TitleCrystal structure of Treponema pallidum TP0796 Flavin trafficking protein, ADP inhibited form
ComponentsThiamine biosynthesis lipoprotein ApbE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / hydrolase / bimetal center / fad pyrophosphatase / flavin turnover / Treponema pallidum / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


FAD:protein FMN transferase / 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
ADENOSINE-5'-DIPHOSPHATE / FAD:protein FMN transferase
Similarity search - Component
Biological speciesTreponema pallidum subsp. pallidum (syphilis treponeme)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3001 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 1.5Sep 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.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: Thiamine biosynthesis lipoprotein ApbE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2194
Polymers36,7431
Non-polymers4763
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.829, 47.252, 57.643
Angle α, β, γ (deg.)90.00, 102.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thiamine biosynthesis lipoprotein ApbE


Mass: 36742.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum subsp. pallidum (syphilis treponeme)
Strain: Nichols / Gene: apbE, tp0796, TP_0796 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O83774
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 293 K / Method: hanging-drop vapor diffusion / 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: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2011 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 13766 / Num. obs: 13766 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.343.40.388194.9
2.34-2.383.50.405194.3
2.38-2.433.50.398196.6
2.43-2.483.70.425198.3
2.48-2.533.70.411198.9
2.53-2.593.90.378199.4
2.59-2.663.90.364199.9
2.66-2.7340.334199.9
2.73-2.814.10.311100
2.81-2.94.10.2321100
2.9-34.10.2191100
3-3.124.10.1741100
3.12-3.264.10.1581100
3.26-3.4440.135199.9
3.44-3.6540.116199.7
3.65-3.933.80.106199.7
3.93-4.333.80.0771100
4.33-4.953.90.06199.1
4.95-6.244.10.0641100
6.24-503.80.046199.7

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Processing

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

4ifu


Resolution: 2.3001→29.654 Å / Occupancy max: 1 / Occupancy min: 0.83 / SU ML: 0.25 / σ(F): 1.36 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 673 4.9 %
Rwork0.1768 --
obs0.1798 13721 98.75 %
all-13718 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.1165 Å2
Refinement stepCycle: LAST / Resolution: 2.3001→29.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 29 158 2687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132587
X-RAY DIFFRACTIONf_angle_d0.7953529
X-RAY DIFFRACTIONf_dihedral_angle_d14.794927
X-RAY DIFFRACTIONf_chiral_restr0.043402
X-RAY DIFFRACTIONf_plane_restr0.002454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.47760.28861350.21292518X-RAY DIFFRACTION96
2.4776-2.72680.25291420.19672566X-RAY DIFFRACTION99
2.7268-3.1210.25521270.1792621X-RAY DIFFRACTION100
3.121-3.93070.21561310.16392653X-RAY DIFFRACTION100
3.9307-29.65650.22191380.1672690X-RAY DIFFRACTION100
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)
10.049-0.03180.00020.0347-0.00110.01770.0215-0.01150.06630.0298-0.0121-0.05630.00060.02220.0609-0.08530.041-0.0350.05240.00470.005353.645546.1832-0.039
20.02960.03810.0180.2445-0.10810.1087-0.0373-0.0650.0510.2169-0.04360.0469-0.1109-0.0623-0.12150.00180.11090.0394-0.1793-0.0845-0.000838.511649.163416.7108
30.06180.0440.03250.0607-0.00470.1156-0.01530.02620.04850.1297-0.00670.1018-0.0154-0.1338-0.00930.0720.00630.04450.0597-0.00730.058731.503339.249827.2096
40.05770.03490.0230.0497-0.05570.25470.0690.0362-0.0123-0.01330.07660.1040.06480.02450.21490.0194-0.03180.0698-0.00290.0523-0.109943.752939.40574.7881
50.032-0.0087-0.03320.2475-0.06380.0692-0.0203-0.0584-0.0066-0.10730.0258-0.03170.0350.0246-0.00010.0285-0.00750.01520.06510.00480.074744.952726.876413.45
60.0754-0.0830.01340.23680.04450.0298-0.0017-0.0293-0.11250.08770.02350.1680.0692-0.01230.0250.0485-0.0013-0.01380.0037-0.02770.032535.775524.61397.5726
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 93 )
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 151 )
4X-RAY DIFFRACTION4chain 'A' and (resid 152 through 225 )
5X-RAY DIFFRACTION5chain 'A' and (resid 226 through 255 )
6X-RAY DIFFRACTION6chain 'A' and (resid 256 through 340 )

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