PDB-4ab4: Structure of Xenobiotic Reductase B from Pseudomonas putida in co...

ID or keywords:

Entry

Database: PDB / ID: 4ab4

Title

Structure of Xenobiotic Reductase B from Pseudomonas putida in complex with TNT

Components

XENOBIOTIC REDUCTASE B

Keywords

OXIDOREDUCTASE / OLD YELLOW ENZYME

Function / homology

Function and homology information

oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / FMN binding / cytosol
Similarity search - Function

Biological species

PSEUDOMONAS PUTIDA KT2440 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Carvalho, A.L. / Mukhopadhyay, A. / Romao, M.J. / Bursakov, S. / Kladova, A. / Ramos, J.L. / van Dillewijn, P.

Citation

Journal: To be Published
Title: Structural Determinants of Aromatic Ring Reduction in the Xenobiotic Reductase B from Pseudomonas Putida
Authors: Carvalho, A.L. / Mukhopadhyay, A. / Bonifacio, C. / Romao, M.J. / Bursakov, S. / Kladova, A. / Ramos, J.L. / Van Dillewijn, P.

History

Deposition	Dec 6, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 19, 2012	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4ab4.cif.gz	282 KB	Display	PDBx/mmCIF format
PDB format	pdb4ab4.ent.gz	224.9 KB	Display	PDB format
PDBx/mmJSON format	4ab4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4ab4_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4ab4_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4ab4_validation.xml.gz	35.7 KB	Display
Data in CIF	4ab4_validation.cif.gz	54.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ab/4ab4 ftp://data.pdbj.org/pub/pdb/validation_reports/ab/4ab4	HTTPS FTP

-
Related structure data

Related structure data	4aeoC 2r14S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4aeo-2 4w86-2 2hs6-2 7l9i-4 5hos-d 7l9f-4 2xm7-d 6d3a-2 6d36-2 6d3a-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: XENOBIOTIC REDUCTASE B

B: XENOBIOTIC REDUCTASE B

hetero molecules

80.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: XENOBIOTIC REDUCTASE B

hetero molecules

defined by author&software
40.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: XENOBIOTIC REDUCTASE B

hetero molecules

defined by author&software
40.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	67.010, 104.870, 106.430
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS oper: (Code: given
Matrix: (0.9999, 0.0095, 0.0097), (0.0101, -0.998, -0.0626), (0.0091, 0.0627, -0.998)
Vector: -33.4947, 1.3063, 3.9597)

-
Protein , 1 types, 2 molecules AB

#1: Protein	XENOBIOTIC REDUCTASE B Mass: 39374.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) PSEUDOMONAS PUTIDA KT2440 (bacteria) / References: UniProt: Q88PD0

-
Non-polymers , 6 types, 835 molecules

#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-TNL / 2,4,6-TRINITROTOLUENE / TNT Mass: 227.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₅N₃O₆
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 824 / 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: 2.38 Å³/Da / Density % sol: 48.4 % / Description: NONE

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 1, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9334 Å / Relative weight: 1
Reflection	Resolution: 1.5→21.4 Å / Num. obs: 111101 / % possible obs: 92.6 % / Observed criterion σ(I): 5 / Redundancy: 7 % / B_iso Wilson estimate: 6.71 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 13.8
Reflection shell	Resolution: 1.5→1.58 Å / Redundancy: 6.2 % / R_merge(I) obs: 0.36 / Mean I/σ(I) obs: 5 / % possible all: 90.2

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R14

2r14

Resolution: 1.5→21.172 Å / SU ML: 0.17 / σ(F): 1.37 / Phase error: 15.07 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.1841	5557	5 %
R_work	0.1602	-	-
obs	0.1614	111027	92.27 %

Solvent computation

Shrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 48.588 Å² / k_sol: 0.41 e/Å³

Displacement parameters

B_iso mean: 9.3 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.1822 Å²	0 Å²	0 Å²
2-	-	1.9835 Å²	0 Å²
3-	-	-	0.1987 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→21.172 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5299	0	131	824	6254

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5593
X-RAY DIFFRACTION	f_angle_d	1.227	7643
X-RAY DIFFRACTION	f_dihedral_angle_d	14.201	2043
X-RAY DIFFRACTION	f_chiral_restr	0.083	817
X-RAY DIFFRACTION	f_plane_restr	0.007	1020

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.5-1.517	0.2248	200	0.1924	3338	X-RAY DIFFRACTION	89
1.517-1.5349	0.2332	155	0.1894	3363	X-RAY DIFFRACTION	90
1.5349-1.5536	0.1852	176	0.1718	3378	X-RAY DIFFRACTION	89
1.5536-1.5733	0.2067	194	0.1781	3380	X-RAY DIFFRACTION	90
1.5733-1.594	0.206	194	0.1725	3400	X-RAY DIFFRACTION	90
1.594-1.6158	0.2027	169	0.1665	3399	X-RAY DIFFRACTION	91
1.6158-1.6389	0.1938	187	0.1634	3425	X-RAY DIFFRACTION	91
1.6389-1.6633	0.1721	182	0.1566	3426	X-RAY DIFFRACTION	91
1.6633-1.6893	0.1795	189	0.1564	3439	X-RAY DIFFRACTION	91
1.6893-1.717	0.1892	183	0.1564	3453	X-RAY DIFFRACTION	91
1.717-1.7466	0.1738	184	0.1512	3474	X-RAY DIFFRACTION	92
1.7466-1.7783	0.1676	171	0.1434	3436	X-RAY DIFFRACTION	91
1.7783-1.8125	0.1892	191	0.1473	3457	X-RAY DIFFRACTION	91
1.8125-1.8495	0.1871	199	0.139	3440	X-RAY DIFFRACTION	92
1.8495-1.8897	0.1657	170	0.1433	3484	X-RAY DIFFRACTION	92
1.8897-1.9336	0.1674	174	0.1524	3474	X-RAY DIFFRACTION	91
1.9336-1.9819	0.1703	187	0.143	3432	X-RAY DIFFRACTION	91
1.9819-2.0355	0.1756	163	0.147	3487	X-RAY DIFFRACTION	91
2.0355-2.0953	0.1848	194	0.1537	3450	X-RAY DIFFRACTION	91
2.0953-2.1629	0.1784	163	0.1471	3459	X-RAY DIFFRACTION	91
2.1629-2.2401	0.1678	167	0.1481	3480	X-RAY DIFFRACTION	91
2.2401-2.3297	0.1764	183	0.1535	3459	X-RAY DIFFRACTION	91
2.3297-2.4356	0.1797	195	0.1543	3453	X-RAY DIFFRACTION	91
2.4356-2.5638	0.1752	185	0.1634	3491	X-RAY DIFFRACTION	91
2.5638-2.7241	0.1597	176	0.1643	3613	X-RAY DIFFRACTION	94
2.7241-2.9339	0.176	189	0.1641	3715	X-RAY DIFFRACTION	96
2.9339-3.2282	0.2046	203	0.1656	3812	X-RAY DIFFRACTION	99
3.2282-3.6932	0.1729	200	0.1563	3865	X-RAY DIFFRACTION	100
3.6932-4.6449	0.1667	212	0.1505	3919	X-RAY DIFFRACTION	100
4.6449-21.1742	0.2367	222	0.21	4069	X-RAY DIFFRACTION	100

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	0.0334	0.011	-0.008	0.0153	-0.0139	0.0329	0.0162	-0.0139	0.0329	-0.0052	0.0036	0.0055	-0.015	-0.016	0.022	0.0216	-0.0024	0.0147	0.008	-0.0032	0.03	-21.2021	8.9226	-2.6495
2	0.0662	0.0107	-0.0047	0.0087	0.0182	0.0548	0.0104	0.0086	0.0252	0.0075	0.0341	0.0221	-0.0264	-0.0148	-0.0227	0.044	-0.0022	0.0096	0.0233	0.0101	0.071	-15.9627	29.8281	-11.7397
3	0.0653	0.0801	-0.0493	0.1089	-0.0347	0.114	0.01	-0.0225	0.0086	0.0077	-0.0033	0.0043	-0.0079	0.003	-0.0039	0.0267	-0.0052	0.0026	0.0426	-0.0154	0.0324	-8.0591	17.3373	5.0856
4	0.0533	0.0097	0.0135	0.0442	0.0129	0.0072	0.0197	-0.0124	0.0081	0.0164	0.0028	-0.0009	-0.0173	0.0119	0.0042	0.0227	-0.0051	0.0063	0.0189	-0.0018	0.0176	-4.0847	13.4308	-8.7959
5	0.0537	-0.0193	-0.0244	0.0305	-0.0108	0.0926	-0.0007	0.0196	-0.003	-0.0174	0.0015	0.0011	0.0033	-0.0086	0.0017	0.0249	-0.0067	0.0109	0.0308	-0.007	0.0059	-8.0518	3.0825	-20.2944
6	0.0404	0.0117	0.0623	0.0412	0.0142	0.111	0.0098	0.0082	-0.0106	-0.002	0.0132	-0.0072	0.008	-0.0046	0.011	0.0233	-0.0129	-0.0023	0.0389	-0.0124	0.0077	-20.1221	-3.759	-17.536
7	0.0818	0.1406	0.0561	0.3063	0.0769	0.045	-0.006	0.0252	0.017	-0.027	0.0043	0.0606	-0.0048	-0.0339	0.0066	0.0375	-0.0062	-0.0133	0.0581	0.005	0.0434	-33.5897	4.2062	-14.5382
8	0.2398	0.0087	0.0357	0.0293	-0.0127	0.0874	-0.0047	0.0271	0.0328	-0.0021	-0.0044	-0.0067	-0.0099	0.0018	0.0055	0.0085	0.0043	-0.0027	0.017	0.0009	0.0289	18.8756	8.6321	13.872
9	0.0412	0.0077	0.0197	0.0019	0.0041	0.0338	0.0179	0.0129	-0.0301	-0.001	0.0054	0.0053	0.0298	-0.021	0.0101	0.0118	-0.0134	-0.0233	0.0124	-0.0003	0.0152	10.8833	-11.5503	4.4863
10	0.162	-0.0011	-0.0016	0.03	0.0508	0.0872	0.0026	-0.0097	-0.0561	-0.0266	0.0372	0.0394	0.0605	-0.0135	-0.0206	0.0855	0.0013	-0.0093	0.0402	0.0127	0.0912	18.0355	-29.2685	13.9265
11	0.061	-0.0345	-0.0255	0.0844	0.0145	0.0107	0.0122	0.0503	-0.0028	-0.0649	-0.0076	-0.0065	0.0325	-0.0014	-0.0019	0.0494	0.0086	0.0016	0.0647	-0.0144	0.0306	25.7008	-16.1251	-1.905
12	0.1055	0.0069	-0.0077	0.0278	-0.0216	0.0512	-0.009	0.0073	0	0.0042	0.0064	-0.0001	0.0199	0.0063	0.001	0.0336	0.0099	-0.008	0.0206	0.0025	0.0208	29.5154	-15.436	8.9862
13	0.0458	-0.0163	0.0232	0.0212	0.0074	0.0267	0.0066	-0.0131	-0.0034	0.012	0.0115	-0.0057	0.0168	0.0076	0.0177	0.0206	-0.0024	-0.0111	0.0369	0.0138	0.0093	28.397	-8.5328	18.5316
14	0.1742	-0.0359	-0.0365	0.0539	-0.015	0.0332	0.0016	-0.0354	0.0171	0.0304	0.0104	0.0023	-0.0113	-0.0216	-0.0038	0.0273	0.0006	-0.0034	0.027	-0.0008	0.0106	18.071	1.661	21.8715
15	0.0077	-0.028	0.0028	0.1138	-0.0008	0.0102	0.0044	-0.0117	0.0116	0.0107	0.0268	0.0348	-0.0028	-0.0312	-0.0147	0.0256	-0.004	0.0108	0.0617	0.0118	0.0317	-0.4227	-4.1605	17.9219

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 2:115)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 116:144)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 145:164)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 165:262)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 263:289)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESSEQ 290:322)
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESSEQ 323:350)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 2:21)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 22:115)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 116:144)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 145:164)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 165:217)
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 218:270)
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESSEQ 271:322)
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESSEQ 323:350)

-
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, 2 molecules AB

-
Non-polymers , 6 types, 835 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, 2 molecules AB

-Non-polymers , 6 types, 835 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, 2 molecules AB

-
Non-polymers , 6 types, 835 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