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

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Basic information

Entry
Database: PDB / ID: 4xdr
TitleCrystal structure of Treponema pallidum TP0796 Flavin trafficking protein, a bifunctional FMN transferase/FAD pyrophosphatase, D284A mutant, ADN 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 / ADENOSINE / FAD:protein FMN transferase
Similarity search - Component
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 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.ptnr2_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)37,65514
Polymers36,6991
Non-polymers95613
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.834, 46.792, 57.725
Angle α, β, γ (deg.)90.000, 102.560, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-532-

HOH

21A-583-

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: 36698.977 Da / Num. of mol.: 1 / Mutation: D284A
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 , 5 types, 207 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Chemical
ChemComp-ACT / ACETATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 194 / 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: 41.29 %
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: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2012 / 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: 1.4→50 Å / Num. obs: 59272 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 15.11 Å2 / Rmerge(I) obs: 0.046 / Χ2: 1.082 / Net I/av σ(I): 25.984 / Net I/σ(I): 14.6 / Num. measured all: 230801
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.4-1.423.20.54528200.87895.6
1.42-1.453.50.46328820.91997.9
1.45-1.483.70.429520.95399.6
1.48-1.513.90.32129820.946100
1.51-1.543.90.27729531.009100
1.54-1.5840.23329810.985100
1.58-1.6240.19829581.05100
1.62-1.6640.16729801.06100
1.66-1.7140.13929351.145100
1.71-1.7640.11829971.177100
1.76-1.8340.09529501.16199.9
1.83-1.940.0830211.159100
1.9-1.9940.06529621.123100
1.99-2.0940.05729611.128100
2.09-2.2240.05129921.121100
2.22-2.3940.04730051.11499.8
2.39-2.633.90.04629781.12399.7
2.63-3.023.90.03729891.17499.4
3.02-3.83.80.03130031.1899.5
3.8-503.90.02629711.13595.7

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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: 1.4→28.163 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 3011 5.08 %random
Rwork0.1715 56250 --
obs0.1728 59261 98.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.32 Å2 / Biso mean: 26.4153 Å2 / Biso min: 7.46 Å2
Refinement stepCycle: final / Resolution: 1.4→28.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2513 0 157 194 2864
Biso mean--32.04 29.34 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142671
X-RAY DIFFRACTIONf_angle_d1.4183613
X-RAY DIFFRACTIONf_chiral_restr0.085424
X-RAY DIFFRACTIONf_plane_restr0.007465
X-RAY DIFFRACTIONf_dihedral_angle_d12.25942
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4003-1.42220.26191150.28172086220181
1.4222-1.44550.26821290.24732502263197
1.4455-1.47040.24141510.22212533268499
1.4704-1.49720.26151460.214926002746100
1.4972-1.5260.20031390.190225432682100
1.526-1.55710.18351520.189425912743100
1.5571-1.5910.22571410.182325472688100
1.591-1.6280.21491320.184425772709100
1.628-1.66870.2161480.171425762724100
1.6687-1.71380.20221270.17125852712100
1.7138-1.76420.19691530.166125722725100
1.7642-1.82120.23361270.171725802707100
1.8212-1.88620.20451290.166525842713100
1.8862-1.96170.19971480.16225982746100
1.9617-2.0510.18091300.157525822712100
2.051-2.15910.17741320.154825982730100
2.1591-2.29430.17031410.152326012742100
2.2943-2.47140.1821400.158525752715100
2.4714-2.71990.21461450.161526022747100
2.7199-3.1130.18381220.17542623274599
3.113-3.92040.18781320.17272624275699
3.9204-28.16910.18841320.17272571270396
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)
12.79970.0645-0.31933.0405-0.10332.32150.0119-0.15880.04620.2627-0.03510.0715-0.07560.07720.00570.0575-0.00320.0010.10680.00480.087351.618651.23423.7699
21.0802-0.194-0.38163.14890.33272.50970.0097-0.13340.18460.41110.0885-0.2442-0.38330.19-0.03890.2151-0.00950.02290.1735-0.03180.153334.594744.776723.4317
30.6052-0.1851-0.04221.1222-0.13780.8907-0.0372-0.0956-0.01330.20480.05490.04010.04220.00230.00040.1036-0.00040.00390.09260.0020.094438.919941.182711.6491
41.3977-0.3986-0.87252.0910.03581.4315-0.0119-0.0245-0.06060.08210.00970.07880.07060.0110.00830.0659-0.0076-0.01520.0753-0.00140.102437.216626.793210.2385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 52 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 114 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 244 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 245 through 340 )A0

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