[English] 日本語
Yorodumi
- PDB-4xdt: Crystal structure of Treponema pallidum TP0796 Flavin trafficking... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
Components

-
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

-
Non-polymers , 6 types, 222 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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 / Acetate


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


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


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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;

-
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: 0

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more