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

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Basic information

Entry
Database: PDB / ID: 4ifx
TitleCrystal structure of Treponema pallidum TP0796 Flavin trafficking protein, FAD substrate bound form
ComponentsThiamine biosynthesis lipoprotein ApbE
KeywordsHYDROLASE / bimetal center / FAD pyrophosphatase / flavin turnover / Treponema pallidum
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
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / FAD:protein FMN transferase
Similarity search - Component
Biological speciesTreponema pallidum subsp. pallidum (syphilis treponeme)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.452 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 1.5Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
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: Thiamine biosynthesis lipoprotein ApbE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6956
Polymers36,7431
Non-polymers9525
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.825, 47.079, 57.583
Angle α, β, γ (deg.)90.00, 102.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-567-

HOH

21A-574-

HOH

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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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*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.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
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: 1.45→50 Å / Num. all: 53215 / Num. obs: 53215 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.45-1.483.30.628195.3
1.48-1.53.60.592196.9
1.5-1.533.80.494197.3
1.53-1.5640.424197.3
1.56-1.64.10.352198.7
1.6-1.634.10.313197.7
1.63-1.674.10.252198
1.67-1.724.10.225199
1.72-1.774.10.182198.4
1.77-1.834.10.143198.4
1.83-1.894.10.109198.7
1.89-1.974.10.093198.7
1.97-2.064.10.065199.1
2.06-2.174.10.058199.3
2.17-2.34.10.05199.5
2.3-2.484.10.043199.5
2.48-2.7340.039199.8
2.73-3.123.90.026199.6
3.12-3.9440.018199.6
3.94-5040.016196.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
PHENIXrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
DENZOdata reduction
HKL-3000data scaling
PHENIXphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4IFU

4ifu


Resolution: 1.452→28.58 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.28 / SU B: 2.554 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20354 2687 5.1 %RANDOM
Rwork0.17237 ---
obs0.17391 50440 97.96 %-
all-53127 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.954 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å21.12 Å2
2---0.22 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.452→28.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2521 0 63 247 2831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192722
X-RAY DIFFRACTIONr_bond_other_d0.0010.022630
X-RAY DIFFRACTIONr_angle_refined_deg2.2281.9883719
X-RAY DIFFRACTIONr_angle_other_deg0.94836006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6825348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.20522.437119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24915424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5781528
X-RAY DIFFRACTIONr_chiral_restr0.1420.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023138
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02647
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.452→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 195 -
Rwork0.302 3488 -
obs--92.35 %
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)
11.06670.24030.00982.0755-0.05922.03440.05310.0440.02840.0432-0.06130.0046-0.02990.10550.00810.0387-0.0053-0.00450.10830.00850.075952.023248.7693.1794
21.09830.5790.40552.960.40362.99020.0159-0.01740.13140.27180.07170.0728-0.40780.0535-0.08760.11180.00430.04960.0395-0.01030.063332.90346.774720.9607
33.0358-1.08640.65816.30321.18534.8490.0676-0.2313-0.13510.89830.1542-0.2550.62770.4731-0.22180.20630.0339-0.03730.089-0.02330.046736.134132.517830.5031
40.2467-0.16730.21310.709-0.1220.189-0.0302-0.05110.01190.10530.02560.1288-0.0238-0.05450.00460.06470.00130.01070.0662-0.00220.082536.504946.427810.7297
51.2294-0.11750.35192.8359-0.72153.2690.0603-0.0591-0.1158-0.0334-0.1364-0.25750.26940.32050.07610.06190.0013-0.00980.0886-0.00920.093146.517429.66470.7781
68.3062-2.43592.54354.4073-0.40832.03360.03510.1783-0.10670.3209-0.0094-0.39580.05880.2533-0.02570.09710.0044-0.02670.04070.00110.054942.6124.245424.914
70.934-0.5569-0.35482.0650.31650.6850.02960.086-0.0553-0.0622-0.06490.18690.0021-0.03420.03540.0473-0.0033-0.01970.0622-0.00520.076235.771524.38925.2261
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 50
2X-RAY DIFFRACTION2A51 - 94
3X-RAY DIFFRACTION3A95 - 133
4X-RAY DIFFRACTION4A134 - 199
5X-RAY DIFFRACTION5A200 - 243
6X-RAY DIFFRACTION6A244 - 266
7X-RAY DIFFRACTION7A267 - 340

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