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

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Basic information

Entry
Database: PDB / ID: 4xdt
TitleCrystal structure of Treponema pallidum TP0796 Flavin trafficking protein, a bifunctional FMN transferase/FAD pyrophosphatase, N55Y mutant, FAD bound form
ComponentsFAD:protein FMN transferase
KeywordsTRANSFERASE / FMN TRANSFERASE / FAD PYROPHOSPHATASE / HYDROLASE / BIMETAL CENTER / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.452 Å
AuthorsTomchick, D.R. / Brautigam, C.A. / Deka, R.K. / Norgard, M.V.
CitationJournal: Mbio / Year: 2015
Title: Evidence for Posttranslational Protein Flavinylation in the Syphilis Spirochete Treponema pallidum: Structural and Biochemical Insights from the Catalytic Core of a Periplasmic Flavin-Trafficking Protein.
Authors: Deka, R.K. / Brautigam, C.A. / Liu, W.Z. / Tomchick, D.R. / Norgard, M.V.
History
DepositionDec 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)38,21915
Polymers36,7921
Non-polymers1,42714
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.777, 46.992, 57.566
Angle α, β, γ (deg.)90.000, 102.210, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-535-

HOH

21A-599-

HOH

DetailsThe biological unit is a monomer. There is 1 biological unit in the asymmetric unit.

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 36792.055 Da / Num. of mol.: 1 / Mutation: N55Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum (strain Nichols) (bacteria)
Strain: Nichols / Gene: apbE, TP_0796 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O83774, FAD:protein FMN transferase

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Non-polymers , 6 types, 222 molecules

#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.1 Å3/Da / Density % sol: 41.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 0.7 M sodium acetate, 0.1 M NaCl, 20% (v/v) ethylene glycol;

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2012 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 53283 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 15.21 Å2 / Rmerge(I) obs: 0.05 / Χ2: 1.118 / Net I/av σ(I): 24.306 / Net I/σ(I): 15.8 / Num. measured all: 224769
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.45-1.4830.5323831.05989.4
1.48-1.53.30.49425711.11696.4
1.5-1.533.70.44526491.15198.5
1.53-1.5640.41726601.10199.8
1.56-1.64.30.38626721.14799.9
1.6-1.634.40.33726781.152100
1.63-1.674.40.27826661.196100
1.67-1.724.50.24126981.208100
1.72-1.774.50.19626751.199100
1.77-1.834.40.1526711.233100
1.83-1.894.40.11326921.184100
1.89-1.974.50.08826911.225100
1.97-2.064.50.06827031.102100
2.06-2.174.50.05826821.007100
2.17-2.34.40.05227011.028100
2.3-2.484.40.05226911.1399.9
2.48-2.734.30.04927121.175100
2.73-3.124.20.0427010.998100
3.12-3.944.20.02727241.01199.8
3.94-504.30.02526630.88695.3

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Processing

Software
NameVersionClassification
HKL-3000data reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4IFU

4ifu


Resolution: 1.452→28.534 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 2701 5.07 %random
Rwork0.1673 50562 --
obs0.1687 53263 98.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.24 Å2 / Biso mean: 27.1384 Å2 / Biso min: 8.61 Å2
Refinement stepCycle: final / Resolution: 1.452→28.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 166 208 2899
Biso mean--40.29 31.67 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0242724
X-RAY DIFFRACTIONf_angle_d1.3143672
X-RAY DIFFRACTIONf_chiral_restr0.078422
X-RAY DIFFRACTIONf_plane_restr0.006469
X-RAY DIFFRACTIONf_dihedral_angle_d14.065978
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4523-1.47870.27241270.2632258238584
1.4787-1.50710.28191430.24992579272296
1.5071-1.53790.24331470.22262615276299
1.5379-1.57130.23021630.209826542817100
1.5713-1.60790.22941300.197427092839100
1.6079-1.64810.23881500.193126592809100
1.6481-1.69260.2311430.178127102853100
1.6926-1.74250.21211530.176126832836100
1.7425-1.79870.24421250.179326962821100
1.7987-1.8630.23881460.171826922838100
1.863-1.93750.18691490.166226472796100
1.9375-2.02570.16791350.153727172852100
2.0257-2.13250.21551400.154326972837100
2.1325-2.2660.16951490.152426792828100
2.266-2.44090.17091400.146726992839100
2.4409-2.68640.17061570.157926942851100
2.6864-3.07470.19141240.164127572881100
3.0747-3.87220.19581400.16127372877100
3.8722-28.53960.18381400.16322680282096
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)
11.16780.28210.02441.528-0.43593.42270.05740.02950.0404-0.0354-0.07530.02750.04150.22650.0620.07160.0039-0.00710.16920.00940.118353.62647.0098-0.4713
21.30750.417-0.82530.8054-0.60111.52890.2022-0.14550.13380.3472-0.08170.0689-0.33490.043-0.07110.23060.00870.0250.1399-0.01250.155438.773350.021816.7279
30.5482-0.2399-0.26151.1676-0.06670.9267-0.0724-0.1361-0.00880.29020.04060.09360.0488-0.02580.0260.14680.00030.00870.1376-0.0080.11635.607841.859819.5535
41.15970.2032-0.01732.4185-1.06122.39890.0773-0.0812-0.0583-0.0823-0.0848-0.11580.2030.26540.05120.13890.0054-0.01720.1664-0.01240.153146.568431.77550.1861
51.0677-0.3737-0.55252.08620.31650.8477-0.0136-0.0134-0.09860.0996-0.02550.12730.09740.01820.0370.1246-0.0051-0.01310.11680.00430.153437.428725.112410.1296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 30 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 92 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 195 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 196 through 244 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 245 through 340 )A0

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