PDB-6unf: Pseudomonas fluorescens isocyanide hydratase post-catalysis at 29...

ID or keywords:

Entry

Database: PDB / ID: 6unf

Title

Pseudomonas fluorescens isocyanide hydratase post-catalysis at 298 K XFEL data

Components

Isonitrile hydratase InhA

Keywords

LYASE / covalent catalytic intermediate

Function / homology

Function and homology information

regulation of DNA-templated transcription
Similarity search - Function

Biological species

Pseudomonas fluorescens (bacteria)

Method

X-RAY DIFFRACTION /

FREE ELECTRON LASER /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Dasgupta, M. / van den Bedem, H. / Wilson, M.A.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis.
Authors: Dasgupta, M. / Budday, D. / de Oliveira, S.H.P. / Madzelan, P. / Marchany-Rivera, D. / Seravalli, J. / Hayes, B. / Sierra, R.G. / Boutet, S. / Hunter, M.S. / Alonso-Mori, R. / Batyuk, A. / ...

History

Deposition	Oct 11, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2019	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
Revision 1.2	Jan 1, 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.identifier_ORCID
Revision 1.3	Oct 11, 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	6unf.cif.gz	322.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6unf.ent.gz	218.8 KB	Display	PDB format
PDBx/mmJSON format	6unf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6unf_validation.pdf.gz	249.3 KB	Display	wwPDB validaton report
Full document	6unf_full_validation.pdf.gz	249.3 KB	Display
Data in XML	6unf_validation.xml.gz	944 B	Display
Data in CIF	6unf_validation.cif.gz	6.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/un/6unf ftp://data.pdbj.org/pub/pdb/validation_reports/un/6unf	HTTPS FTP

-
Related structure data

Related structure data	6ni4C 6ni5C 6ni6C 6ni7C 6ni9C 6niaC 6npqC 6undC 3nonS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6npq-d 7ldm-1 6foq-1 7lav-1 6und-d 6a6v-1 6xcq-d 3pew-d 5l77-d 7lax-1 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	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Isonitrile hydratase InhA

B: Isonitrile hydratase InhA

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

1

Idetical with deposited unit
defined by author&software
Evidence: equilibrium centrifugation

Unit cell

Length a, b, c (Å)	56.806, 57.637, 68.762
Angle α, β, γ (deg.)	90.000, 112.740, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Isonitrile hydratase InhA Mass: 24180.646 Da / Num. of mol.: 2 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: inhA, PFL_4109 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4K977
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Isonitrile hydratase InhA

Mass: 24180.646 Da / Num. of mol.: 2
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: inhA, PFL_4109 / Plasmid: pET15b / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4K977

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.15 Å³/Da / Density % sol: 42.7 %
Crystal grow	Temperature: 298 K / Method: batch mode / pH: 8.8 Details: 31% PEG 3350, 250 mM MgCl2, 125 mM Tris-HCl, 2 mM DTT

-
Data collection

Diffraction	Mean temperature: 298 K / Serial crystal experiment: Y
Diffraction source	Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.3 Å
Detector	Type: RAYONIX MX340-HS / Detector: CCD / Date: Nov 12, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.3 Å / Relative weight: 1
Reflection	Resolution: 1.55→20.1 Å / Num. obs: 60082 / % possible obs: 99.9 % / Redundancy: 44.1 % / B_iso Wilson estimate: 18.47 Å² / CC_1/2: 0.937 / R split: 0.232 / Net I/σ(I): 73.1
Reflection shell	Resolution: 1.55→1.57 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2988 / CC_1/2: 0.36 / R split: 0.658 / % possible all: 100
Serial crystallography sample delivery	Method: injection
Serial crystallography sample delivery injection	Description: coMESH
Serial crystallography data reduction	Crystal hits: 16893 / Frames indexed: 14483

-
Processing

Software

Name	Version	Classification
cctbx.xfel		data reduction
cctbx.prime		data scaling
PHENIX	1.16_3549	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3non

3non

Resolution: 1.55→17.46 Å / SU ML: 0.1486 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.3667

	R_factor	Num. reflection	% reflection
R_free	0.1945	1995	3.35 %
R_work	0.1693	-	-
obs	0.1701	59499	99.96 %

Solvent computation

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

Displacement parameters

B_iso mean: 26.51 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→17.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3368	0	0	270	3638

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0068	3587
X-RAY DIFFRACTION	f_angle_d	0.8544	4928
X-RAY DIFFRACTION	f_chiral_restr	0.0529	577
X-RAY DIFFRACTION	f_plane_restr	0.0058	663
X-RAY DIFFRACTION	f_dihedral_angle_d	13.3757	2165

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 (%)
1.55-1.59	0.2843	143	0.2698	4079	X-RAY DIFFRACTION	99.95
1.59-1.63	0.2801	139	0.243	4092	X-RAY DIFFRACTION	99.98
1.63-1.68	0.2596	143	0.2308	4076	X-RAY DIFFRACTION	99.98
1.68-1.73	0.2618	142	0.2213	4084	X-RAY DIFFRACTION	100
1.73-1.8	0.234	145	0.2126	4095	X-RAY DIFFRACTION	99.98
1.8-1.87	0.2294	136	0.1935	4089	X-RAY DIFFRACTION	100
1.87-1.95	0.252	144	0.1821	4098	X-RAY DIFFRACTION	100
1.95-2.06	0.1976	136	0.1746	4101	X-RAY DIFFRACTION	100
2.06-2.18	0.1794	144	0.1622	4100	X-RAY DIFFRACTION	99.98
2.18-2.35	0.1676	138	0.1606	4107	X-RAY DIFFRACTION	99.98
2.35-2.59	0.2066	148	0.1557	4114	X-RAY DIFFRACTION	100
2.59-2.96	0.1791	142	0.1602	4118	X-RAY DIFFRACTION	100
2.96-3.72	0.1736	146	0.1488	4149	X-RAY DIFFRACTION	100
3.72-17.46	0.1729	149	0.1587	4202	X-RAY DIFFRACTION	99.66

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	1.62901058956	0.399490953307	-0.444348313678	1.58574019289	-0.299411566172	1.80010908897	0.00898757089566	0.164027397642	0.151048595725	-0.0534429517374	0.0710316285496	0.177702536081	-0.195444355775	-0.165906804606	-0.053517731275	0.128670104665	0.0191150017951	-0.00592401993994	0.128510468054	0.016611096929	0.149072201764	-1.95451220148	24.525170159	21.358526093
2	4.60187730131	2.64299156972	2.15427432245	4.66101920692	4.87403510278	5.32542520783	0.0406363588739	0.312382758106	0.111495476491	-0.305783692011	-0.10813359922	0.359163547261	-0.37970795326	-0.618081958953	0.259423091752	0.19349396642	0.0501721783298	0.0166152006071	0.298271904169	0.0302362531853	0.278716383215	-13.8817368183	24.6771507871	27.0742186746
3	1.20063929978	0.0756263211609	-1.13605018997	1.28541235312	-0.238013413193	2.36969867224	-0.0439965054025	0.0787188667281	-0.0534364614093	0.00177751152202	0.00786643898711	0.185463416481	0.168981916576	-0.225473313344	0.032291525745	0.140004070094	-0.0285721223646	0.00145981130323	0.148114131204	-0.00156929639986	0.169508691349	-6.56965695964	9.53470342661	26.6154882988
4	2.36571828111	-1.41777949045	-2.13396753112	0.921748465699	1.13477362916	2.63850632613	0.179873286368	0.223429004895	-0.0692856889061	-0.37223709523	-0.0959524123158	0.350947715345	0.151477423785	-0.443405905858	-0.0727827714748	0.215105014806	-0.0448005242851	-0.0515468912967	0.235353787488	-0.0169418757811	0.206060141714	-3.65631546677	9.83368206293	4.15589383295
5	1.17633733102	-0.745967207155	0.520961905222	1.46934166845	-1.44484742054	6.59070151022	-0.0430833869878	-0.182641905502	-0.0586275117499	0.0636861101061	0.130246699196	-0.0550613956443	0.262632281146	0.0485552110229	-0.0874361644695	0.122911490815	0.00823239736818	-0.00258496082073	0.132817940498	0.0163289821998	0.173642939161	11.6604080073	2.88350621243	26.8964843565
6	3.32724531676	-4.42324121305	-1.96777759054	6.48134579766	1.28000297934	4.66463589645	-0.106906983114	-0.27275584726	0.102266026877	0.308905450981	0.0883774727962	0.0581566089214	0.105262791755	-0.177152990912	-0.00466721742464	0.27777964968	0.00560822807183	0.00435943123542	0.199515117372	-0.0108073252779	0.146127850524	-2.39732679698	15.8798015514	42.8332103614
7	2.70285681303	0.0155898431862	-1.1555044598	3.56867342964	-0.885182920557	1.00252980997	-0.0130910497912	-0.383634380814	0.0119567615024	0.255428471532	0.0028069741254	-0.340775340699	-0.143757906903	0.191516319924	0.0201328728893	0.162166399053	-0.0189451633809	-0.0152040842501	0.190192952844	-0.0175396664853	0.171181481539	18.1319220957	20.9847765848	17.9442132639
8	6.28060683136	-0.917510207865	0.635191589416	1.27929363634	1.71121877738	5.51058806783	0.00519238131527	-0.22827195728	0.268803069084	-0.193325309668	0.143836531009	-0.140647523172	-0.49497515779	0.0591907642228	-0.135901939558	0.212329008658	3.58251472136E-6	0.00623350733723	0.118419912909	-0.00149064962658	0.170433077124	11.5032789126	30.8849203517	11.6825029039
9	1.38138564839	0.0588149317688	-0.846621399112	1.93121069692	-0.0458898240245	1.46045490002	-0.0151642669451	-0.152531916069	0.188684922634	-0.163243484644	0.0108911441831	-0.214504253769	-0.23386138872	0.137467562156	0.023103124941	0.199314062996	-0.0306395043417	0.0105862899735	0.180520751536	-0.0154215045715	0.225905360094	21.9338342299	25.3752834019	8.55811232598
10	7.8583144163	-4.2900196449	4.1048227081	6.11680406156	-1.58962613216	5.42367300267	0.0912129320872	-0.222479709502	0.142630471446	0.0542239160455	-0.0200834894688	-0.349991797069	-0.14103219396	0.307239835883	-0.0525516700159	0.128912505364	-0.0382130114013	0.019277195668	0.202498893252	0.0119891126582	0.215223112584	29.4524605308	24.0406851667	7.16154552265
11	1.95597387811	0.517759170021	-0.7475439801	2.06922685152	0.0966007158653	2.5600264667	-0.131803317109	0.133108242203	-0.283429872373	-0.255566658746	0.00882864795862	-0.233850222456	0.175214595522	0.0670050403311	0.117933096718	0.181894326046	0.018106874247	0.047889366305	0.140714867317	-0.00931204766891	0.191532175977	19.9979330376	11.0356017428	0.542655981892
12	3.64349329375	2.71717485491	-1.98942829972	4.03625901063	0.296674529906	2.80694095981	-0.211184067364	-0.349405706998	-0.364830462166	0.0449064685894	0.0671942560878	-0.625286045284	0.247848636167	0.358085666992	0.112919550605	0.203328309885	0.0567159045175	0.0374157077894	0.179689902244	0.00259421182779	0.257572719501	23.5716870683	8.25239647298	7.9471458862
13	2.35229307513	-0.00131815961445	-0.193699611637	1.8411044446	-1.19216413799	2.69749732013	-0.0793234524971	-0.170097719954	-0.150661018628	0.0326236836381	-0.158155061979	-0.322965882968	0.0635990185569	0.509962343917	0.226229712556	0.132216013843	0.0197115788204	-0.0148969847149	0.170981142757	0.0302681116136	0.186280945643	17.6663717168	7.63945059617	20.6087069383
14	1.7267884014	0.663955032204	0.068476024189	1.46880728195	-0.315610388083	6.98433025887	-0.0476959249298	0.240943975063	-0.0411538161941	-0.411373658116	0.0813182659143	0.0616040329376	0.437119608473	-0.379625849914	-0.0333903437486	0.252861307963	-0.00399305263792	-0.0246113191846	0.169277761054	-0.0249276843956	0.1858719511	1.64399039738	5.24243364177	3.49516300772
15	2.08101827448	3.57312340741	1.00985330304	7.05925424353	-0.012943729198	5.85053864633	-0.309647524299	0.472917392131	0.209218177341	-0.338961561677	0.338788772702	0.231284529101	-0.429888421619	-0.0634520909872	-0.0707228149801	0.331287938204	-0.0283040092635	0.0382145667197	0.190146350351	0.0120372651715	0.172923518949	17.5247193954	20.0447160463	-10.1055737373

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 80 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 81 through 95 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 96 through 166 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 167 through 178 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 179 through 207 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 208 through 227 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid -2 through 36 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 37 through 53 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 54 through 80 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 81 through 95 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 96 through 139 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 140 through 151 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 152 through 178 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 179 through 207 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 208 through 227 )

-
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