PDB-6le2: Structure of D-carbamoylase mutant from Nitratireductor indicus

ID or keywords:

Entry

Database: PDB / ID: 6le2

Title

Structure of D-carbamoylase mutant from Nitratireductor indicus

Components

N-carbamoyl-D-amino-acid hydrolase

Keywords

HYDROLASE / carbamoylase / hydantoinse process / D-amino acid / BIOSYNTHETIC PROTEIN

Function / homology

Function and homology information

hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
Similarity search - Function

Biological species

Nitratireductor indicus C115 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.14 Å

Authors

Ni, Y. / Liu, Y.F. / Xu, G.C. / Dai, W.

Funding support

China, 1items

Citation

Journal: Acs Catalysis / Year: 2020
Title: Structure-Guided Engineering of D-Carbamoylase Reveals a Key Loop at Substrate Entrance Tunnel
Authors: Liu, Y. / Xu, G. / Zhou, J. / Ni, J. / Zhang, L. / Hou, X. / Yin, D. / Rao, Y. / Zhao, Y.L. / Ni, Y.

History

Deposition	Nov 23, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 28, 2020	Provider: repository / Type: Initial release
Revision 1.1	May 12, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Nov 22, 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	6le2.cif.gz	319.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6le2.ent.gz	216.6 KB	Display	PDB format
PDBx/mmJSON format	6le2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6le2_validation.pdf.gz	3.1 MB	Display	wwPDB validaton report
Full document	6le2_full_validation.pdf.gz	3.1 MB	Display
Data in XML	6le2_validation.xml.gz	26.3 KB	Display
Data in CIF	6le2_validation.cif.gz	36.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/le/6le2 ftp://data.pdbj.org/pub/pdb/validation_reports/le/6le2	HTTPS FTP

-
Related structure data

Related structure data	6lcgC 6ledC 6leiC 1fo6S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6lei-d 2aum-d 5nkk-2 5zl6-2 2c16-d 1bd0-d 1gzg-d 4z8l-1 5jd5-5 6m1w-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: N-carbamoyl-D-amino-acid hydrolase

B: N-carbamoyl-D-amino-acid hydrolase

hetero molecules

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

1

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

Unit cell

Length a, b, c (Å)	95.320, 95.320, 258.570
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22
Space group name Hall	P6₁2(x,y,z+5/12)
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/6 #3: y,-x+y,z+5/6 #4: -y,x-y,z+1/3 #5: -x+y,-x,z+2/3 #6: x-y,-y,-z #7: -x,-x+y,-z+2/3 #8: -x,-y,z+1/2 #9: y,x,-z+1/3 #10: -y,-x,-z+5/6 #11: -x+y,y,-z+1/2 #12: x,x-y,-z+1/6

#1: Protein	N-carbamoyl-D-amino-acid hydrolase Mass: 35495.086 Da / Num. of mol.: 2 / Mutation: D187N,A200N,S207A,R211G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitratireductor indicus C115 (bacteria) Gene: NA8A_19058 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K2NMS4
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.43 Å³/Da / Density % sol: 49.33 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 4000, Sodium phosphate pH 6.5, Sodium chloride

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
Detector	Type: BRUKER SMART 6500 / Detector: CCD / Date: Nov 11, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 2.14→47.66 Å / Num. obs: 39298 / % possible obs: 100 % / Redundancy: 38.2 % / B_iso Wilson estimate: 46.35 Å² / R_merge(I) obs: 0.124 / Net I/σ(I): 23.7
Reflection shell	Resolution: 2.14→2.2 Å / Redundancy: 20.7 % / R_merge(I) obs: 2.364 / Num. unique obs: 39380 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
PHENIX	1.17_3644	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1FO6

1fo6

Resolution: 2.14→47.66 Å / SU ML: 0.2812 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.1861

	R_factor	Num. reflection	% reflection
R_free	0.2287	1977	5.03 %
R_work	0.1802	-	-
obs	0.1827	39279	99.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 56.29 Å²

Refinement step

Cycle: LAST / Resolution: 2.14→47.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4877	0	56	211	5144

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0072	5090
X-RAY DIFFRACTION	f_angle_d	0.838	6852
X-RAY DIFFRACTION	f_chiral_restr	0.0543	715
X-RAY DIFFRACTION	f_plane_restr	0.0053	903
X-RAY DIFFRACTION	f_dihedral_angle_d	23.7491	1899

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 (%)
2.14-2.19	0.3241	129	0.2776	2596	X-RAY DIFFRACTION	99.89
2.19-2.25	0.34	146	0.2611	2601	X-RAY DIFFRACTION	99.96
2.25-2.32	0.3282	137	0.252	2619	X-RAY DIFFRACTION	99.93
2.32-2.39	0.3153	117	0.2374	2628	X-RAY DIFFRACTION	99.82
2.39-2.48	0.2807	152	0.2249	2574	X-RAY DIFFRACTION	99.89
2.48-2.58	0.302	126	0.2062	2670	X-RAY DIFFRACTION	100
2.58-2.7	0.2856	136	0.2099	2610	X-RAY DIFFRACTION	99.96
2.7-2.84	0.2777	148	0.2193	2638	X-RAY DIFFRACTION	99.93
2.84-3.02	0.2893	138	0.2185	2642	X-RAY DIFFRACTION	100
3.02-3.25	0.2445	152	0.2046	2651	X-RAY DIFFRACTION	100
3.25-3.58	0.2469	140	0.1893	2684	X-RAY DIFFRACTION	99.96
3.58-4.09	0.2203	141	0.1482	2706	X-RAY DIFFRACTION	100
4.09-5.16	0.1555	159	0.1294	2736	X-RAY DIFFRACTION	99.97
5.16-47.66	0.1902	156	0.1676	2947	X-RAY DIFFRACTION	99.68

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	4.43690994968	0.314831576994	2.31234539692	1.98124980325	-0.319386836568	5.99288645697	0.193046387555	-0.0711311995907	-0.3878117198	0.192126476603	0.0100488423499	-0.0499795481752	0.258160343279	-0.421835681361	-0.227232823719	0.380932724054	-0.11324387108	-0.0444568627115	0.407520272042	-0.0328428456978	0.467464855785	-28.1368898943	-23.646924571	0.985038986704
2	4.59445334735	-3.44700780161	5.13993791018	4.08753139551	-3.28413863679	5.91139639252	-0.106517517577	-1.10806215137	-0.315307558426	0.132199359585	0.405683818801	0.432969052514	0.532674684911	-1.80955291988	-0.42533472278	0.361980042195	-0.111966353639	-0.015152380636	0.660563761017	0.0405061667011	0.561953814021	-39.2581092753	-16.3626756379	-1.33375785848
3	2.99352325673	-0.351547811458	-0.551508413508	1.8706217385	-0.979914304416	5.51410320201	0.115769977965	0.115709070677	0.156598949813	-0.0821188132001	-0.0716042161563	0.0527452154193	-0.172655806677	-0.309166171679	-0.0501602855824	0.301618673818	0.00300930266653	-0.0504866165657	0.247510076191	0.0077292931312	0.314324255691	-29.3406447569	-7.90075589362	-10.2054170362
4	2.17425962759	-0.0121315892605	1.37793902534	2.31347598545	-1.29924243981	3.86137734263	0.106990742205	0.445653975017	0.124994099253	-0.326510265131	-0.0696496331037	0.012644866006	0.124535043915	0.0232787904468	-0.0848915555074	0.408175633196	0.0699047494915	0.0291530934483	0.386567746033	0.0118105132895	0.367037151474	-22.9304638915	-11.538082165	-18.7649117219
5	4.16059709412	-0.548763359703	-1.03421612663	2.46339461105	-1.56089886153	1.652662224	0.0184483436266	0.408820540364	-0.229246536926	-0.341363935564	0.020359915292	-0.126006489813	0.287746646005	0.0132596304013	-0.0645349952466	0.404378147549	-0.0138706127211	-0.0421046453335	0.26595395698	0.0217109599993	0.349754787557	-17.7610791151	-19.4857182017	-11.7475939237
6	5.46357106297	-4.81537538454	-2.7476322895	8.81938603149	-2.69514474284	7.14107326121	0.0120214731258	0.0575272177499	-0.194145523897	-0.629411991123	-0.0246074090851	0.607660077659	0.25686637332	-0.787641671767	-0.0674920040467	0.507285913706	-0.112322795984	-0.00189875131088	0.243866078415	0.0446036669622	0.380253428809	-17.2535480668	-29.3608581151	-12.9589816305
7	9.01457853149	-2.23335746736	4.01451741487	2.41246695705	-0.747083124216	4.66583391303	0.218177871661	0.481250626387	-0.0919206553926	-0.256600186753	-0.103238091716	0.184452784508	0.515840093432	-0.165819567585	-0.197530965214	0.403087424039	-0.0648191355666	-0.0584149652342	0.308215318857	0.0457009896184	0.367217663773	-26.4548713631	-23.8414755216	-10.9667457964
8	5.14557591979	-1.23504385935	-0.329046054415	2.67455520082	-0.650765509821	3.5611782237	0.202653674589	-0.182497985588	-0.641029026686	0.118668876564	0.0703676832209	-0.0383623145817	0.650527093551	0.123311119639	-0.276227095694	0.546842766949	-0.0772723955327	-0.079651704099	0.2640528981	0.0264937510852	0.354680421152	-19.7366077427	-27.2923645253	0.228194346106
9	7.66575853398	0.490436335896	-1.71835825692	7.55682833037	0.309296179761	7.39608057964	-0.377372471666	-0.316556019756	0.428834878034	0.407352581951	0.197409525314	-0.829709388535	0.394982137524	0.153281626588	0.21295578886	0.355404504921	-0.00637514241825	-0.0324849513325	0.301920607778	-0.0769822684275	0.594726786446	2.07476843043	-18.2609150417	-10.9322214
10	5.00185757678	-0.869149902429	-1.97687731248	7.24951471724	-0.382451130385	0.849399133968	0.0770464178947	0.604538098966	-0.702762398176	-0.665785223767	0.142481929538	0.240905807301	1.08271577253	0.286948479076	-0.353785071997	0.584159337971	0.0448377342251	0.167982110232	0.352320732408	-0.0488740310237	0.320948098566	4.96744962929	-44.3199284491	-21.6249068089
11	7.93533131817	0.96316073987	6.54128806341	0.484700325076	-0.373231638253	9.8600749523	-0.00986830072747	0.221951317041	-0.487671777989	-0.294482139845	0.0212228494867	-0.13000771815	0.84848575835	0.321390279845	-0.093554201937	0.944608911757	0.148249899081	0.180672544206	0.330296997543	0.0522205155224	0.587914664176	11.7518448259	-51.1436717668	-22.2694829237
12	2.97760581773	-0.185625140627	1.61520809579	2.42749863335	-0.29379012724	5.50627098694	-0.262188623982	-0.0418526274898	0.031518673501	-0.179299765693	-0.0837560855494	-0.385566694706	0.267370054285	0.610155621357	0.322841790041	0.584753719414	0.134028510169	0.0876421677049	0.410236403233	0.0808106022584	0.498831675013	16.3818047277	-39.2428376676	-13.5996065401
13	2.78030052971	-0.377024320928	0.354231316954	2.82013754612	0.22696835658	3.86130269619	-0.0382140263935	0.0502612736147	0.149746054134	-0.209408701973	-0.0583210485106	-0.436677584853	0.34075290196	0.395544725239	0.0865735177605	0.380352223548	0.0616046344607	0.0841663829964	0.275210719715	0.0653799928668	0.42934069108	11.2504907219	-31.3798407287	-17.1431313839
14	6.08550440046	-0.397284862515	-2.08580440917	2.11350615037	1.72170451184	2.28038903787	-0.0868977521478	-0.333192390906	-0.0918815307181	0.0533211242523	0.0140852854235	-0.0280391839789	0.768969208926	0.103110275318	0.0875236687406	0.547197552627	-0.0197850424876	-0.0150250528586	0.258406373419	-0.00641155498027	0.427698420852	-3.92631888629	-35.4678528326	-11.3031606499
15	4.97529408435	-1.48728033871	1.68688352032	0.420637350308	-0.639115153961	5.21258586516	-0.171054555666	-0.0509861808146	-0.649132548871	0.0684460278087	0.260518055911	-0.000681973017301	0.666524185357	0.0747145107778	-0.0942944133816	0.602482630237	0.0392032226655	0.01852683048	0.239035187427	0.0301951744086	0.344975877174	1.39649914987	-40.7419092734	-12.9047601639
16	6.23280286777	-2.93605784834	-0.427624737069	7.45618447459	-0.449447774035	4.7181644892	-0.0577411860962	0.569226368989	-0.468908435763	-0.949766822366	-0.0132776272451	0.614411592887	0.922613064227	-0.448190081397	0.0360002283328	0.634263223727	-0.12030665789	0.00994024701269	0.368247652945	-0.0755337661964	0.396064041115	-7.13419560648	-39.3346333707	-23.8763629995
17	4.69225202652	-0.076868894722	2.92672616152	2.25374224235	0.776115912117	3.29702427845	0.632864311233	0.25784193183	-0.484171005822	-0.267831920212	0.323308938995	-0.239806754607	0.824548054016	-0.581034066216	-0.83381727714	0.65288336687	-0.11505823026	-0.00907532264404	0.42105228119	0.117566845254	0.682582543551	-9.38806499643	-13.4047000919	-18.9955559529

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -8 through 20 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 21 through 37 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 38 through 135 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 136 through 163 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 164 through 207 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 208 through 225 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 226 through 251 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 252 through 282 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 283 through 304 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 20 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 21 through 37 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 38 through 77 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 78 through 186 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 187 through 225 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 226 through 251 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 252 through 282 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 283 through 307 )

-
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