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

ID or keywords:

Entry

Database: PDB / ID: 4xdu

Title

Crystal structure of Treponema pallidum TP0796 Flavin trafficking protein,a bifunctional FMN transferase/FAD pyrophosphatase, N55Y mutant, ADP bound form

Components

FAD:protein FMN transferase

Keywords

TRANSFERASE / 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

Biological species

Treponema pallidum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.35 Å

Authors

Tomchick, D.R. / Brautigam, C.A. / Deka, R.K. / Norgard, M.V.

Citation

Journal: 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

Deposition	Dec 20, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4xdu.cif.gz	206.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4xdu.ent.gz	164.8 KB	Display	PDB format
PDBx/mmJSON format	4xdu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xd/4xdu ftp://data.pdbj.org/pub/pdb/validation_reports/xd/4xdu	HTTPS FTP

-
Related structure data

Related structure data	4xdrC 4xdtC 4ifu C: citing same article (ref.)
Similar structure data	4xdr-d 4xdt-d 5evj-1 3atu-d 5c4l-2 4ifx-d 6rtx-d 5ex5-1 6dws-1 1hjo-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: FAD:protein FMN transferase

hetero molecules

37.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	116.830, 46.814, 57.501
Angle α, β, γ (deg.)	90.000, 102.220, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-646- HOH
2	1	A-713- HOH

Details

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

-
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

#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, 265 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.09 Å³/Da / Density % sol: 41.11 %
Crystal grow	Temperature: 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

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97918 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2012 / Details: monochromator

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 1.3→50 Å / Num. obs: 72901 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / B_iso Wilson estimate: 12.79 Å² / R_merge(I) obs: 0.048 / Χ²: 0.987 / Net I/av σ(I): 22.914 / Net I/σ(I): 12.7 / Num. measured all: 269463

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
1.3-1.32	1.7	0.509	2361	0.762	64
1.32-1.35	2.1	0.51	3116	0.696	82.9
1.35-1.37	2.5	0.523	3535	0.817	94.5
1.37-1.4	2.9	0.482	3678	0.922	98.7
1.4-1.43	3.3	0.437	3767	0.816	99.9
1.43-1.46	3.7	0.368	3732	0.772	100
1.46-1.5	3.9	0.314	3725	0.842	100
1.5-1.54	4	0.239	3740	0.836	100
1.54-1.59	4	0.2	3732	0.794	100
1.59-1.64	4.1	0.168	3747	0.829	100
1.64-1.7	4.1	0.136	3771	0.84	100
1.7-1.76	4.1	0.112	3724	0.867	100
1.76-1.84	4.1	0.088	3759	0.932	100
1.84-1.94	4.1	0.077	3764	1.328	100
1.94-2.06	4.1	0.055	3750	1.138	100
2.06-2.22	4.1	0.053	3774	1.265	100
2.22-2.45	4.1	0.052	3764	1.262	99.9
2.45-2.8	4	0.042	3782	1.335	99.9
2.8-3.53	4	0.029	3820	1.119	100
3.53-50	4.1	0.025	3860	0.955	99.3

-
Processing

Software

Name	Version	Classification
HKL-3000		data reduction
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Resolution: 1.35→24.535 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.79 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.188	3361	5.05 %	random
R_work	0.1674	63237	-	-
obs	0.1685	66598	99.64 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 94.41 Å² / B_iso mean: 23.6365 Å² / B_iso min: 6.98 Å²

Refinement step

Cycle: final / Resolution: 1.35→24.535 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2525	0	87	255	2867
B_iso mean	-	-	24.92	29.26	-
Num. residues	-	-	-	-	330

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	2664
X-RAY DIFFRACTION	f_angle_d	1.243	3586
X-RAY DIFFRACTION	f_chiral_restr	0.074	416
X-RAY DIFFRACTION	f_plane_restr	0.005	462
X-RAY DIFFRACTION	f_dihedral_angle_d	13.561	953

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.35-1.3693	0.2541	112	0.2618	2540	2652	95
1.3693-1.3897	0.2788	139	0.2484	2553	2692	98
1.3897-1.4114	0.2996	137	0.2336	2619	2756	100
1.4114-1.4346	0.2271	130	0.2136	2629	2759	100
1.4346-1.4593	0.2097	158	0.2044	2633	2791	100
1.4593-1.4858	0.2222	147	0.1892	2595	2742	100
1.4858-1.5144	0.1968	151	0.1827	2621	2772	100
1.5144-1.5453	0.1829	144	0.1717	2629	2773	100
1.5453-1.5789	0.1996	159	0.1734	2616	2775	100
1.5789-1.6156	0.2226	122	0.1736	2652	2774	100
1.6156-1.656	0.2148	152	0.1717	2639	2791	100
1.656-1.7008	0.2181	143	0.1658	2629	2772	100
1.7008-1.7508	0.1871	148	0.1671	2617	2765	100
1.7508-1.8073	0.2091	125	0.1643	2648	2773	100
1.8073-1.8719	0.1899	142	0.1617	2639	2781	100
1.8719-1.9468	0.1826	147	0.1593	2634	2781	100
1.9468-2.0354	0.1935	127	0.1524	2652	2779	100
2.0354-2.1426	0.1883	140	0.1552	2636	2776	100
2.1426-2.2768	0.1518	143	0.1471	2632	2775	100
2.2768-2.4524	0.1535	143	0.151	2677	2820	100
2.4524-2.699	0.1708	151	0.1628	2616	2767	100
2.699-3.0889	0.2006	124	0.1653	2703	2827	100
3.0889-3.8891	0.1691	136	0.1682	2699	2835	100
3.8891-24.5386	0.1849	141	0.1636	2729	2870	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.3108	0.5391	-0.887	2.934	-0.7928	4.7559	0.0519	0.0318	0.0295	-0.0604	-0.0663	-0.0058	0.1207	0.2545	0.0681	0.0293	0.0053	0.0161	0.1088	0.0015	0.0828	-4.7697	21.5985	-0.1304
2	1.5914	0.3976	-1.4025	0.4372	-0.8123	1.9195	0.2194	-0.1824	0.111	0.3059	-0.0689	0.0602	-0.3679	0.0945	-0.1161	0.2197	0.0088	0.05	0.1292	-0.0133	0.1393	-19.4716	24.8181	16.7005
3	3.2731	-0.3168	0.1822	3.1388	0.5563	4.5794	0.0025	-0.4489	-0.2153	0.7901	0.1712	-0.2706	0.4948	0.4863	-0.068	0.3106	0.0269	0.0253	0.2468	-0.0232	0.1646	-21.6506	7.7939	30.376
4	0.5264	-0.2844	0.2535	0.9128	-0.3463	0.2321	-0.0519	-0.0335	-0.0069	0.0937	0.0451	0.0656	-0.0091	-0.0444	0.0091	0.0908	-0.003	0.0243	0.076	-0.0004	0.0882	-20.7098	19.9238	8.5214
5	0.5382	0.008	-0.1995	1.8718	-1.1254	3.1021	-0.0128	-0.0888	-0.046	0.1606	-0.024	-0.1034	0.1239	0.2293	0.0469	0.1071	-0.001	-0.0055	0.0982	-0.0058	0.1047	-15.782	1.851	13.8032
6	1.2423	-0.6319	-0.4608	2.3212	0.3088	1.0267	0.0318	0.1135	-0.1214	-0.0488	-0.072	0.2275	0.0656	-0.0563	0.0384	0.0842	-0.0117	-0.0017	0.0799	-0.0103	0.0975	-22.6979	-0.5073	4.4554

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 30 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 31 through 92 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 93 through 131 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 132 through 216 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 217 through 279 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 280 through 340 )	A

-
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

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

+
Jul 12, 2017. Major update of PDB

-
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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 1 molecules A

-
Non-polymers , 6 types, 265 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 1 molecules A

-Non-polymers , 6 types, 265 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 1 molecules A

-
Non-polymers , 6 types, 265 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi