PDB-6wjb: UDP-GlcNAc C4-epimerase from Pseudomonas protegens in complex wit...

ID or keywords:

Entry

Database: PDB / ID: 6wjb

Title

UDP-GlcNAc C4-epimerase from Pseudomonas protegens in complex with NAD and UDP-GlcNAc

Components

NAD-dependent epimerase/dehydratase family protein

Keywords

ISOMERASE / Short Chain Dehydrogenase /

Complex / NAD dependent

Function / homology

Function and homology information

nucleotide binding
Similarity search - Function

Biological species

Pseudomonas fluorescens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Marmont, L.S. / Pfoh, R. / Robinson, H. / Howell, P.L.

Funding support

Canada, 1items

Citation

Journal: J.Biol.Chem. / Year: 2020
Title: PelX is a UDP-N-acetylglucosamine C4-epimerase involved in Pel polysaccharide-dependent biofilm formation.
Authors: Marmont, L.S. / Whitfield, G.B. / Pfoh, R. / Williams, R.J. / Randall, T.E. / Ostaszewski, A. / Razvi, E. / Groves, R.A. / Robinson, H. / Nitz, M. / Parsek, M.R. / Lewis, I.A. / Whitney, J.C. ...

History

Deposition	Apr 13, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 8, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 15, 2020	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Sep 2, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6wjb.cif.gz	295.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6wjb.ent.gz	200.3 KB	Display	PDB format
PDBx/mmJSON format	6wjb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wj/6wjb ftp://data.pdbj.org/pub/pdb/validation_reports/wj/6wjb	HTTPS FTP

-
Related structure data

Related structure data	6wj9C 6wjaC 1sb8S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6wj9-d 6i1h-d 7cnx-1 5upk-d 1lpa-d 4gj5-d 6pmh-1 6ltt-d 4xhr-d 1wl9-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

Deposited unit

A: NAD-dependent epimerase/dehydratase family protein

B: NAD-dependent epimerase/dehydratase family protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	123.040, 75.455, 79.156
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab

Components on special symmetry positions

ID	Model	Components
1	1	A-555- HOH
2	1	A-591- HOH

#1: Protein	NAD-dependent epimerase/dehydratase family protein / PelX Mass: 32668.877 Da / Num. of mol.: 2 / Mutation: C232S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (bacteria) Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: PFL_2971 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4KCF6
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical	ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₇N₃O₁₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.81 Å³/Da / Density % sol: 56.26 % / Description: Stacked flat square plate crystals
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2 M ammonium sulphate, 0.1 M sodium citrate pH 5.6, 25% (w/v) PEG 4000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.075 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 43495 / % possible obs: 100 % / Redundancy: 11.4 % / B_iso Wilson estimate: 33.4 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 38.8
Reflection shell	Resolution: 2.1→2.18 Å / Redundancy: 14.6 % / R_merge(I) obs: 0.58 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 4230 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
DENZO		data reduction
SCALEPACK		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1SB8

1sb8

Resolution: 2.1→49.92 Å / SU ML: 0.206 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.0125
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1969	1976	4.59 %
R_work	0.1668	41051	-
obs	0.1682	43027	98.84 %

Solvent computation

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

Displacement parameters

B_iso mean: 41.13 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→49.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4503	0	140	217	4860

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0062	4733
X-RAY DIFFRACTION	f_angle_d	0.8813	6465
X-RAY DIFFRACTION	f_chiral_restr	0.0477	752
X-RAY DIFFRACTION	f_plane_restr	0.0046	836
X-RAY DIFFRACTION	f_dihedral_angle_d	14.5855	2799

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 (%)
2.1-2.16	0.2576	138	0.1857	2753	X-RAY DIFFRACTION	94.6
2.16-2.21	0.2546	128	0.18	2866	X-RAY DIFFRACTION	97.97
2.21-2.28	0.2355	152	0.1737	2880	X-RAY DIFFRACTION	98.22
2.28-2.35	0.2218	134	0.1711	2847	X-RAY DIFFRACTION	98.29
2.35-2.44	0.2332	144	0.1745	2890	X-RAY DIFFRACTION	98.22
2.44-2.53	0.2321	139	0.1738	2910	X-RAY DIFFRACTION	98.96
2.53-2.65	0.2305	134	0.1772	2903	X-RAY DIFFRACTION	99.05
2.65-2.79	0.2322	134	0.1753	2943	X-RAY DIFFRACTION	99.26
2.79-2.96	0.2195	148	0.1848	2925	X-RAY DIFFRACTION	99.45
2.96-3.19	0.2166	143	0.1854	2958	X-RAY DIFFRACTION	99.84
3.19-3.51	0.2042	140	0.1814	2979	X-RAY DIFFRACTION	99.9
3.51-4.02	0.1837	147	0.1579	2997	X-RAY DIFFRACTION	100
4.02-5.07	0.139	141	0.1368	3024	X-RAY DIFFRACTION	100
5.07-49.92	0.1763	154	0.1631	3176	X-RAY DIFFRACTION	99.91

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	2.86431990783	-0.757783853694	-0.317289277583	1.42801698454	0.0264887713141	2.12311775661	0.0798644015539	-0.210020599702	-0.473100160195	-0.322206411954	-0.140935578602	-0.778177398457	0.447530876415	0.391580896382	0.0594792954065	0.34020204094	0.11603609277	0.109520059525	0.311180904348	0.0633945747181	0.685361232968	62.7826988965	48.2879500213	2.58656629209
2	6.56066567232	1.17635964514	-0.103579119218	2.68874538269	0.299489045021	1.06471573632	-0.0583299922861	-0.157237573248	-0.598143814142	-0.230818500001	-0.0826862950476	-0.352531316836	0.245681036242	-0.053093477234	0.107089352544	0.279627584514	0.046003497754	0.0237190974074	0.207069608654	0.0533865336617	0.330346764323	47.050567979	49.4450125427	7.89439908019
3	0.665417125379	1.14277205129	-1.06462492509	3.58682639828	-1.13713605811	2.0209504451	-0.0839161594462	0.181649838186	0.0611955354387	-0.10151053501	0.173915785071	0.0423508431961	-0.0342678514736	-0.0413063648595	-0.0624292201583	0.171841757027	0.0281940385534	0.0105865503715	0.214659046539	-0.0253330540087	0.226997080765	44.7888773281	64.697354543	2.64325590253
4	1.7952500737	0.396964888436	-0.865182268012	1.97739433598	-0.351710956899	1.3254320541	0.0691191392294	-0.179033657853	0.096877231372	0.0405143964571	-0.108213490182	-0.31327657802	0.0657951637772	0.149962177538	0.066460648205	0.176575277951	0.0392467828931	0.00955382474783	0.249264844338	-0.00259369708584	0.302720855854	49.5258327502	60.645770765	8.82212135485
5	5.54416693548	0.2724733175	1.10165647067	2.85849428186	0.466756861496	5.37181799743	-0.220922123181	0.397922800317	-0.698324975749	-0.450988778867	-0.151210894876	0.066205374709	1.67330392221	-0.648972967658	0.297515730556	0.891850423485	-0.0935338981588	0.258302371377	0.335191295255	-0.153291285199	0.605627059774	48.8084630541	51.0034746081	-16.3823580574
6	2.28702071499	-0.277766950204	-0.388935149435	1.90934965935	-0.780324928095	1.91034975388	-0.0728644557058	0.123778711718	-0.163883012936	-0.435689766663	-0.0829071657716	-0.295305379718	0.254672645453	0.111232247328	0.0665971027521	0.301559539031	0.00321858945632	0.102442246731	0.173656499681	-0.0400407711616	0.384179179753	51.6327425243	63.3472945697	-8.38349860139
7	3.119114269	0.421683472837	2.55487810393	3.04819973319	-0.416404776049	2.28880121201	-0.293317369258	1.55746673649	-0.64909469198	-1.0011635859	-0.0794212715476	0.173154852912	0.834675872408	-0.229137323079	0.260564000543	0.832458217097	-0.137950568288	0.12997246648	0.57724080329	-0.189974655739	0.409603275995	45.1178005991	58.9243240407	-26.8143309669
8	6.35400758698	-0.761398698129	1.97174040792	1.67291358949	0.0950721077542	6.80449668444	0.0615823303323	0.163827870245	-0.166827483535	-0.124003204812	-0.173620437795	0.1814152991	0.62739823375	-0.874240230499	0.0791505903672	0.341164986355	-0.0561605150218	0.0365454654577	0.364784158533	-0.0693561742816	0.270083899517	38.7254047738	64.9211088055	-10.5211620676
9	3.45846414803	1.45848655623	2.58488603014	3.30973336964	2.45605424785	6.84308000216	0.00636419253297	0.571420955711	0.0850246015084	-0.485844773093	0.220145981251	-0.670495580133	-0.0528556041302	0.793796123192	-0.199174042515	0.353286924591	0.01183979771	0.108923707814	0.346130166893	0.0379832535723	0.400331531715	57.6466813929	65.9002066434	-11.2968490549
10	0.852464764573	-0.84701558162	-0.883947798083	3.93221336529	-0.0348238903729	3.6491655706	-0.11152558443	-0.0560077699266	-0.0517866335465	0.658570080199	0.0105271143575	0.412623150737	0.509314528088	-0.418823428472	0.0940280159413	0.379147184221	-0.100207849078	0.0603271185185	0.348842802374	0.00649014018319	0.252704891915	22.0609439411	45.0897632327	25.6542006889
11	5.99261892042	2.2823895703	-0.267605396024	3.80816486933	-0.61727532792	3.51490197476	0.114070205273	-0.452545475536	-0.202277717738	0.379283897163	-0.273494384247	-0.379992603608	0.0434378731638	0.22124647332	0.121889453309	0.283655231191	0.00219961840935	-0.00347537124796	0.243199978065	0.0564911293427	0.200846145216	36.7068910531	50.032536036	19.218670455
12	1.5416339898	-0.445984009788	-1.61155060516	3.87647872076	0.390219645428	2.01218251675	0.0514834314119	-0.0984345123052	0.319644230235	-0.1475825967	0.0112466606189	-0.00671861234505	-0.244437844098	-0.099582525508	-0.0539100966945	0.276210578363	-0.013021167341	-0.0108633474209	0.304087694515	0.0195255131493	0.216762983024	32.0647891551	65.259858376	16.4586904962
13	0.89662574331	0.192175293353	0.0443103101321	2.77258357973	1.16445957222	3.16108721143	-0.0518388479455	0.0328781625578	-0.00357868881918	-0.0572127203888	-0.0159822907299	0.156729748262	-0.0593877447883	-0.201662886577	0.0686081994467	0.19501034558	-0.0250396462265	-0.00659372063336	0.259552370518	0.0215404015474	0.185928128875	30.1695995244	57.5455897177	13.5527608645
14	1.71533505417	2.05955845258	1.97768724535	3.30528529805	2.81791853949	4.17799617722	0.0814916291095	0.0158016111817	-0.0988493930766	0.474972201227	0.0696011286021	-0.0800409275582	0.303696326029	0.0443314187141	-0.172004959206	0.374104159614	0.0869777685221	0.0784927862655	0.352789105874	0.00777303818213	0.296293917058	29.2593784654	63.9177329475	35.6447826916
15	0.555102324811	0.821706445104	1.58850108766	2.04799266034	1.90575311957	5.79473834054	-0.0620285068772	0.115486220044	0.0646296012167	0.124081994879	0.0717143744224	0.0570463682854	-0.0270863952701	0.292579420133	-0.0415524159196	0.318726128585	0.114608269063	0.0473630450933	0.32322526897	-0.00271293420123	0.292206887153	30.3389935707	71.3265930644	32.5788249713
16	2.87536362599	-0.092949083792	2.54665828896	1.93584817749	-0.711858116596	9.83890745179	0.163528412961	-0.0929346112211	0.297685442129	0.274187402238	-0.0197051586631	0.507225071189	-0.559614640756	-1.22087228638	-0.149558370486	0.386499122134	0.0644294290174	0.0831270432283	0.507282121629	-0.0414296773375	0.47146231592	18.8169373099	67.9266003157	29.9407216235

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 76 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 77 through 111 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 112 through 144 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 145 through 177 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 178 through 199 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 200 through 249 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 250 through 270 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 271 through 284 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 285 through 310 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 3 through 76 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 77 through 111 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 112 through 144 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 145 through 177 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 178 through 231 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 232 through 284 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 285 through 310 )

-
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

-
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

-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

-
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