PDB-6und: Pseudomonas fluorescens isocyanide hydratase thioimidate intermed...

ID or keywords:

Entry

Database: PDB / ID: 6und

Title

Pseudomonas fluorescens isocyanide hydratase thioimidate intermediate 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

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Download

PDBx/mmCIF format	6und.cif.gz	321.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6und.ent.gz	218.5 KB	Display	PDB format
PDBx/mmJSON format	6und.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6und_validation.pdf.gz	963.3 KB	Display	wwPDB validaton report
Full document	6und_full_validation.pdf.gz	964.9 KB	Display
Data in XML	6und_validation.xml.gz	20.6 KB	Display
Data in CIF	6und_validation.cif.gz	29.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/un/6und ftp://data.pdbj.org/pub/pdb/validation_reports/un/6und	HTTPS FTP

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Related structure data

Related structure data	6ni4C 6ni5C 6ni6C 6ni7C 6ni9C 6niaC 6npqC 6unfC 3nonS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ni4-1 7lav-1 6unf-d 7ldo-1 6foq-1 7ldi-1 7lb9-1 7ldm-1 6npq-d 5msu-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

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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

hetero molecules

48.7 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)	56.766, 57.424, 68.790
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

#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: Chemical	ChemComp-QCV / N-(4-nitrophenyl)methanimine Mass: 150.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₆N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.47 %
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

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Data collection

Diffraction	Mean temperature: 298 K / Serial crystal experiment: N
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: 60053 / % possible obs: 99.9 % / Redundancy: 53 % / B_iso Wilson estimate: 18.49 Å² / CC_1/2: 0.963 / R split: 0.197 / Net I/σ(I): 58.4
Reflection shell	Resolution: 1.55→1.57 Å / Redundancy: 5.5 % / Num. unique obs: 2970 / CC_1/2: 0.14 / R split: 0.905 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
cctbx.xfel		data reduction
cctbx.prime		data scaling
PHENIX	1.16_3549	phasing
PHENIX	1.16_3549	refinement
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3non

3non

Resolution: 1.55→20.1 Å / SU ML: 0.1723 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0357

	R_factor	Num. reflection	% reflection
R_free	0.1908	1986	3.35 %
R_work	0.1633	-	-
obs	0.1642	59214	99.86 %

Solvent computation

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

Displacement parameters

B_iso mean: 26.83 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→20.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3368	0	22	269	3659

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0047	3560
X-RAY DIFFRACTION	f_angle_d	0.7785	4881
X-RAY DIFFRACTION	f_chiral_restr	0.0479	572
X-RAY DIFFRACTION	f_plane_restr	0.0049	652
X-RAY DIFFRACTION	f_dihedral_angle_d	12.7161	2131

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	0.3141	141	0.322	4036	X-RAY DIFFRACTION	99.05
1.59-1.63	0.306	140	0.2869	4069	X-RAY DIFFRACTION	99.88
1.63-1.68	0.3279	143	0.2587	4076	X-RAY DIFFRACTION	99.93
1.68-1.73	0.2636	138	0.2387	4023	X-RAY DIFFRACTION	100
1.73-1.8	0.2575	147	0.2287	4106	X-RAY DIFFRACTION	99.93
1.8-1.87	0.2484	134	0.2029	4073	X-RAY DIFFRACTION	100
1.87-1.95	0.2375	144	0.185	4094	X-RAY DIFFRACTION	100
1.95-2.06	0.2119	135	0.1742	4071	X-RAY DIFFRACTION	100
2.06-2.18	0.1945	145	0.1575	4101	X-RAY DIFFRACTION	100
2.18-2.35	0.1711	142	0.1517	4078	X-RAY DIFFRACTION	100
2.35-2.59	0.1786	141	0.1505	4100	X-RAY DIFFRACTION	99.98
2.59-2.96	0.2004	142	0.1591	4105	X-RAY DIFFRACTION	100
2.96-3.73	0.1792	146	0.136	4129	X-RAY DIFFRACTION	100
3.73-20.1	0.1327	148	0.1311	4167	X-RAY DIFFRACTION	99.24

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	1.88371478753	0.519517321001	-0.445062491195	1.6000495038	-0.458806852291	1.7936928195	0.0161123401932	0.204624513093	0.168789530191	-0.0302608040614	0.0671703062119	0.205275450646	-0.1826490461	-0.183047375931	-0.0447510547675	0.118022432644	0.0186535545777	-0.00480114731829	0.121521624055	0.0133000856336	0.137803360936	-1.93429049899	24.5516599311	21.2082146441
2	6.68322473301	3.28352636419	3.72939996243	7.30258886709	5.17428064529	4.95195819348	-0.00382838197656	0.238154517219	0.224269560484	-0.397549401575	-0.0939909928288	0.501287419183	-0.426435519509	-0.78006814104	0.143283266887	0.153938870834	0.0341136475319	0.00109611286279	0.274081977016	0.052740082081	0.211478372609	-13.8651888785	24.5906840307	27.067329429
3	2.85850905086	0.0299831763455	-0.780392930649	3.01671970978	-0.599920407541	2.45775976499	-0.0809695727926	-0.0329360634938	-0.148660951081	0.0207281198818	0.027386066232	0.162221904175	0.21586280779	-0.115334283839	0.0569390876277	0.107174886831	-0.0285032118048	0.00820675896608	0.101199900703	-0.00969453142943	0.109337538776	-6.40473225985	9.48856683731	30.9844726425
4	3.8221166266	-2.39787215125	-3.72623875349	6.3916013218	0.354984995798	4.4341299654	-0.323217577424	0.58721084783	-0.0839181983777	-0.301177573869	0.24103835447	0.29880619346	0.234032643508	-0.571462815411	0.0797561127176	0.213890505811	-0.0765870709906	-0.011743745921	0.210350058211	0.0231167343289	0.217898247217	-9.96684985969	8.79025020058	22.9714593028
5	5.28343448709	-0.766120068361	0.894708370647	2.67469756105	1.14234310514	3.96206719011	-0.00952086023633	0.031105305954	-0.0881805743853	-0.0893677734681	-0.105592826944	0.438430115763	0.0839858870983	-0.529976897964	0.0958284818299	0.212877216499	-0.050148792356	-0.00707284993788	0.175722570877	-0.0298460925684	0.248670941632	-4.1972580933	9.93295102515	10.2278227966
6	1.21702783966	-0.772490616243	0.781577280543	2.17206982796	-1.97878660866	2.5476217678	0.00360841548898	-0.0874680429106	-0.0339172666638	0.0160849056809	0.0511395520937	-0.0102330374072	0.404424536078	0.0297132524981	-0.0761296712495	0.103065088441	0.0163188610413	0.0012905005544	0.148376938896	0.00197087797469	0.161707847799	11.7250575653	2.58208252241	26.0063470776
7	5.76174896858	-4.77663214673	-2.30180573022	4.22583944726	1.23337622715	6.0454535438	0.00549419573561	-0.458987038693	-0.0755609961204	0.376456765753	0.111982813029	0.0356426715473	0.148149599083	-0.0452195829313	-0.0346632854296	0.257357011138	-0.0054620705481	0.00457719851799	0.168964728205	-0.0197790206099	0.158931329689	-2.35992633558	15.9396188543	43.0118731203
8	6.45300541748	-0.231906484419	0.773510003076	4.34943403328	-0.681721312334	2.24763803932	-0.129390687739	-0.461024742713	0.051639618743	0.287467076142	0.107072148485	-0.420915284911	-0.305958781468	0.125661160237	0.102586876909	0.165273704934	-0.0196677708587	0.00688116077884	0.144685028475	-0.0371112778036	0.159097487788	20.089385543	23.3024271218	16.0795679276
9	1.24333310697	-0.215315700946	-1.38956473209	5.10765962336	-1.46350854773	2.86043610271	-0.0276224134905	-0.353513475821	-0.0324898336714	0.341068409932	-0.0322336626761	-0.320749733716	-0.0945559862176	0.246978616859	0.0607974548882	0.111030766676	0.00554362850246	-0.0017540110801	0.181195323556	-0.000852524359345	0.114324407686	16.0977810079	19.2232574793	19.0445789584
10	5.65168973328	1.2194716866	2.43540493823	2.87824857114	2.76632822831	6.67737180013	-0.0546089881269	-0.190453655271	0.386818151799	-0.104293439107	0.0899342801948	-0.098407780234	-0.429450083443	0.015673036261	-0.0117162956163	0.188092709991	0.0202226620883	-0.00369018041264	0.107352948382	0.00294820939544	0.162066514327	11.5106758584	30.8372479632	11.6784355596
11	2.35319530555	-0.00356581974484	-0.627781899177	2.29701385928	0.151584958427	1.70919433277	0.00435179976242	-0.165782952322	0.222531235769	-0.123227233357	-0.015293654052	-0.265928426857	-0.217558131844	0.0966561695464	0.0465600983364	0.159042390791	-0.0208306070687	0.0155399418342	0.131180003659	-0.00779970434586	0.184159149828	21.5738837041	25.3582519577	8.25413617473
12	5.25899660792	-6.08994218311	5.8095068351	9.01479482923	-5.29890828669	8.39421255834	0.0477383594422	0.077935961814	0.193722361118	-0.153583528643	-0.156960874715	-0.490830362653	-0.032220530612	0.464865393506	0.0780378169433	0.118474191615	-0.0372407931887	0.0239768689053	0.196713041665	0.0241766819318	0.228754053296	29.5478209135	23.9551431859	6.80206758584
13	3.97398207724	1.51700488505	-0.719336288564	2.01401702771	1.22791801273	3.12251463634	-0.0705258660988	-0.0105903234017	-0.132947235111	-0.141772175306	0.0160354475406	-0.171554597788	0.152362435248	0.0769744950075	0.036424580275	0.136592963832	0.0216562785303	0.034941552726	0.114756170954	0.00318685457752	0.147176412323	20.9905932211	15.9246170119	4.87049678533
14	4.48840103449	-1.00559622911	-0.394831049327	6.02127038966	0.920081381708	2.65814367655	-0.151838897276	0.166928076766	-0.541983827591	-0.221224343412	0.0275966432716	-0.703898348923	0.178827345928	0.249328449209	0.121445677518	0.164923424525	0.0371805912381	0.0514292582071	0.152738143358	-0.00206054015671	0.184091316537	23.8162491344	11.2183101499	0.420842480414
15	4.62287459873	0.0389016168958	-1.31421415688	1.7062384106	0.199711357719	1.86594158826	-0.1170317393	0.119859432267	-0.385034411368	-0.110709490397	0.0241593576853	-0.20182792543	0.282380550887	0.044623129641	0.0594844374084	0.20232457019	0.0175892014023	0.0422297782966	0.104122435117	-0.0375117649954	0.218017974969	19.5293908032	8.41920992032	1.39476327546
16	9.03600099383	-0.251778902911	5.66462778939	3.19853525254	-0.976490875849	3.94701684091	-0.077582064321	-0.0923141267864	-0.049222273707	-0.13622507394	-0.0661129855483	-0.345975449882	0.0572039739375	0.141159552492	0.087832262723	0.172118210435	0.0195495021066	0.0302813911739	0.192050798965	0.0249520189162	0.193886042663	17.5885116958	9.05959665725	15.527762118
17	6.25379217566	1.33214971379	-2.3673536612	1.35844451501	-1.58310085182	1.96979531093	0.214202417993	-0.314819042662	0.17947314552	0.175247458867	-0.265852287724	-0.395690566133	-0.0100027553803	0.420007320016	0.0768540410358	0.158302733786	0.0302770385846	-0.0199866253884	0.215186311521	0.0533170548435	0.218838880411	17.7209393108	6.00821365617	26.3361987266
18	1.38977230511	0.201164165555	0.49151312407	1.73751141168	-1.09511275755	8.86742736507	-0.0263042958903	0.121235368605	-0.0598108849969	-0.415489336159	0.029619816134	0.0361374299459	0.57678628347	-0.308479949243	-0.0291850477071	0.218568946676	-0.0236631848522	-0.0100177744891	0.146734039176	-0.0311228202832	0.173794443054	1.53659156669	5.147219421	4.0576524967
19	3.74604821641	5.7478656693	0.41442267212	9.66599958527	-0.429439492791	5.89764864144	-0.332931858032	0.637111879197	0.230851042271	-0.57935595961	0.321202972638	0.187635104004	-0.209263609867	-0.0298729909915	0.0169628866379	0.317723079991	-0.0299393956304	0.0308818171677	0.213116622329	0.00663386772552	0.123670628321	17.5802663295	20.2076330265	-10.1538168051

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 139 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 140 through 151 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 152 through 178 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 179 through 207 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 208 through 227 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid -2 through 14 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 15 through 36 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 37 through 53 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 54 through 80 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 81 through 95 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 96 through 109 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 110 through 121 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 122 through 151 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 152 through 166 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 167 through 178 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 179 through 207 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 208 through 227 )

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-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