PDB-6npq: Pseudomonas fluorescens isocyanide hydratase at 298 K XFEL data

ID or keywords:

Entry

Database: PDB / ID: 6npq

Title

Pseudomonas fluorescens isocyanide hydratase at 298 K XFEL data

Components

Isonitrile hydratase InhA

Keywords

LYASE / ThiJ/PfpI / DJ-1 superfamily

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.

Funding support

United States, 1items

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	Jan 18, 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: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_audit_support.funding_organization
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	6npq.cif.gz	322.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6npq.ent.gz	218.7 KB	Display	PDB format
PDBx/mmJSON format	6npq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	6ni4C 6ni5C 6ni6C 6ni7C 6ni9C 6niaC 6undC 6unfC 3nonS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6unf-d 6foq-1 7lav-1 6ni4-1 6fyg-1 6foq-2 6xcq-d 4j1q-d 6fyf-1 5xao-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)	56.879, 57.677, 68.778
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) / Strain (production host): BL21(DE3) / References: UniProt: Q4K977
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 298 / 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) / Strain (production host): BL21(DE3) / References: UniProt: Q4K977

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.17 Å³/Da / Density % sol: 43.22 %
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→20.13 Å / Num. obs: 60075 / % possible obs: 99.9 % / Redundancy: 50.5 % / B_iso Wilson estimate: 18.38 Å² / CC_1/2: 0.962 / R split: 0.196 / Net I/σ(I): 60.5
Reflection shell	Resolution: 1.55→1.57 Å / Redundancy: 6.3 % / Num. unique obs: 2983 / CC_1/2: 0.16 / R split: 0.862 / % possible all: 99.8
Serial crystallography measurement	Focal spot size: 5 µm² / Pulse photon energy: 9.5 keV / XFEL pulse repetition rate: 10 Hz
Serial crystallography sample delivery	Description: coMESH / Method: injection
Serial crystallography sample delivery injection	Flow rate: 0.3 µL/min / Injector diameter: 100 µm
Serial crystallography data reduction	Frame hits: 23669 / Frames indexed: 21834

-
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→20.13 Å / SU ML: 0.2031 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.374

	R_factor	Num. reflection	% reflection
R_free	0.1865	2002	3.36 %
R_work	0.1595	-	-
obs	0.1604	59628	99.93 %

Solvent computation

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

Displacement parameters

B_iso mean: 27.69 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→20.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3368	0	0	298	3666

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0046	3558
X-RAY DIFFRACTION	f_angle_d	0.7765	4883
X-RAY DIFFRACTION	f_chiral_restr	0.0484	574
X-RAY DIFFRACTION	f_plane_restr	0.0054	654
X-RAY DIFFRACTION	f_dihedral_angle_d	12.8924	2143

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	0.3319	144	0.311	4079	X-RAY DIFFRACTION	99.46
1.59-1.63	0.3194	143	0.2769	4109	X-RAY DIFFRACTION	99.98
1.63-1.68	0.2758	142	0.2448	4086	X-RAY DIFFRACTION	99.91
1.68-1.73	0.2491	142	0.2234	4079	X-RAY DIFFRACTION	100
1.73-1.8	0.2408	147	0.2095	4090	X-RAY DIFFRACTION	99.98
1.8-1.87	0.239	132	0.1916	4130	X-RAY DIFFRACTION	99.98
1.87-1.95	0.219	147	0.177	4088	X-RAY DIFFRACTION	100
1.95-2.06	0.1895	135	0.1705	4106	X-RAY DIFFRACTION	100
2.06-2.18	0.1788	146	0.1569	4111	X-RAY DIFFRACTION	100
2.18-2.35	0.1596	138	0.1448	4127	X-RAY DIFFRACTION	100
2.35-2.59	0.1846	148	0.1494	4120	X-RAY DIFFRACTION	99.98
2.59-2.96	0.1718	142	0.1539	4119	X-RAY DIFFRACTION	100
2.96-3.73	0.1771	146	0.1384	4164	X-RAY DIFFRACTION	100
3.73-20.13	0.1504	150	0.1293	4218	X-RAY DIFFRACTION	99.82

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	2.35835755692	-0.496673734052	-0.903037584215	3.07130316213	0.480338928563	2.16088451543	0.0532003997858	0.328984105044	0.101116860151	-0.186434524225	0.0308333987621	0.157466254138	-0.0989388611928	-0.187491475668	-0.0676470248732	0.116188191067	-0.011386507739	-0.0115638383188	0.145056686128	0.0295706067209	0.137353858798	-1.97030254014	21.6743187991	16.7026637243
2	7.91919703806	-0.466631032438	0.312205792827	1.22726364696	-1.97258691019	3.6372050273	0.112457891848	0.13501352946	0.453014426655	0.134461052797	-0.0298611397038	0.00829095152985	-0.328150111608	-0.0418101082803	-0.0744330611652	0.188316593314	-0.0103544647235	-0.00073273077598	0.0954305029288	-0.0222208451905	0.149435964663	4.48209251231	30.0399018137	23.5408768823
3	1.08464088682	1.18935222657	-0.802091464475	1.78925793738	-0.228598963311	1.76991810375	0.0218633337178	0.1152151037	0.235923317738	0.0474859878122	0.0839757226427	0.315167340726	-0.274575802005	-0.183340815685	-0.0697854947668	0.14046361438	0.0362642939118	0.000120131762661	0.142788576163	0.0202069618479	0.180319261466	-6.01706152342	24.7573027898	26.0976936634
4	6.23404014996	2.60799625899	2.88829874612	8.19342709338	5.45155688033	8.34932750868	-0.0355154893138	0.268817778251	0.200534386755	-0.161922627435	-0.0466398517106	0.383662156067	-0.345696061885	-0.757213730395	0.108808987331	0.135379673012	0.0416491910603	0.0218561235031	0.261308668351	0.0543762046912	0.210935282759	-13.8702203628	24.6863895667	27.0874125238
5	1.71166159071	-0.282587001515	-0.660054985882	3.19016098756	-0.180346835585	2.39258472635	-0.0116415361106	0.0719185531354	-0.0356414015315	0.0812056097294	0.00754155477801	0.237899150066	0.114358114316	-0.230521388272	0.00770739545515	0.118442951121	-0.0207717093709	0.00257022167021	0.150938060047	-0.00398068123426	0.144736811257	-8.60871513739	12.6674515588	29.4963776189
6	3.61488457184	0.153963282962	-1.46042480019	2.26119669271	-0.480625855914	2.02544005823	-0.10993479434	0.081342394223	-0.0397054992674	-0.00545815826957	0.0217445826916	0.208395136438	0.185002808444	-0.108249830538	0.0606967175809	0.155958962394	-0.0247113709881	0.0148798867447	0.128997894774	0.00113713704112	0.177463913304	-6.09391094244	6.98002301603	29.3206087974
7	8.3561197753	-2.08903628217	5.3994363752	3.49831702514	-1.25314135204	3.58587824808	-0.0489112697547	-0.109455019641	-0.0362318709336	-0.076741007828	-0.0266507577542	0.336391977743	0.0319971401025	-0.414184573814	0.0646606100531	0.173970868725	-0.00952701251022	0.00525917479915	0.202052492817	-0.00183454832217	0.183885646338	-4.07422163549	10.3019663585	15.6034763128
8	2.29542201554	-1.56311318081	-1.49325186728	1.09534350582	0.974478673752	2.25929786692	0.0958901309091	0.14361010293	0.0640728893614	-0.292057153134	-0.0492312729109	0.26194492302	-0.00733704735774	-0.292161459627	-0.0803898366521	0.230751859028	-0.0377176327359	-0.0464941658528	0.241859472599	-0.0264688402192	0.224475209627	-3.65426074659	9.82899732867	4.15180410451
9	1.55619367805	-0.896012483304	1.22570511646	1.39136496187	-2.09518393181	6.77534351647	-0.0639747033728	-0.132097329416	-0.0637737200161	0.042436312648	0.0805998643512	-0.0261017856679	0.147069660877	0.0637533719518	-0.0157851840187	0.15004160581	0.0137657252163	-0.00390811961277	0.135012551912	0.00505422844209	0.190674031103	11.9195995691	2.93496699511	26.4268227337
10	2.99813926432	-4.4842748378	-1.28865451698	6.91362361748	0.952841714366	4.69588242642	-0.0433014168353	-0.248143896355	0.0753249678639	0.403135290505	0.121346904441	0.0199702083056	0.232217798381	-0.110350244571	-0.0616428696869	0.279766187941	0.000821570517551	0.00453230983788	0.196844954323	-0.00951127785619	0.16046687687	-2.3780216778	15.8849455878	42.8557717411
11	6.32412806918	-0.363333239839	0.939600642906	3.873054562	-0.826996028559	2.0998701331	-0.175943993379	-0.445870456718	0.0560123745961	0.321942550479	0.0538635124922	-0.385175039714	-0.268082116683	0.0766305192547	0.200522502112	0.207272778055	-0.0166670849741	-0.00168727452449	0.16361892359	-0.0264718171503	0.174522281936	20.0880474705	23.3638867811	16.0587847071
12	1.17551129253	0.736512507708	-1.76149681096	4.626046797	-1.06530386212	2.75633411518	0.0321345914886	-0.358834216728	-0.124156622378	0.291791687066	-0.108469547998	-0.26265808445	-0.0273494562865	0.271741072811	0.0924027866566	0.147907834289	0.00335823211987	-0.0124287888894	0.207341876229	0.0102615379977	0.15004161471	16.6327884631	19.1425020837	19.4309444958
13	8.19807317978	0.174288566814	1.21008701082	1.89076391191	1.84799015767	5.06568225854	-0.0429335679599	-0.391260832832	0.443224987072	-0.12349515305	0.109451991927	-0.0223710411142	-0.49058834962	0.0419688499139	-0.0960119716646	0.230114076557	0.00720897421003	-0.00516008202947	0.11475794347	-0.000188146788974	0.169653811123	11.5166858402	30.9018106171	11.6713982831
14	2.75094990665	0.403622552751	-0.447900262644	2.08043643127	0.0755454780256	2.19541660654	0.0121739855991	-0.146427114847	0.104450328279	-0.105553854225	-0.0457521117843	-0.209136364095	-0.158383073442	0.200887299972	0.0306117828043	0.141094274638	-0.0107424967809	0.0159146258577	0.137543985169	-0.0020009111081	0.168310884733	23.8119593169	22.7416198562	7.14757366221
15	2.95249135531	-0.432422153736	0.160791751804	5.09838243544	0.311186990044	1.87443711649	-0.183640644206	-0.00228428356293	-0.551215031563	-0.291416577419	0.00195148271553	-0.754793835645	0.17869419989	0.24069019982	0.195539227744	0.203283378432	0.0401336292364	0.0618173500643	0.16197461831	-0.00755951119229	0.232696961387	23.8898055021	11.1892311503	0.449878399302
16	3.54871335829	0.567408682762	-1.5142194273	1.47993829812	0.417168426471	1.65983218992	-0.145809560263	0.105088091258	-0.316436694274	-0.189644821679	0.0367620119456	-0.259144296749	0.225033254026	0.0356184406732	0.0735211278174	0.229591947932	0.0247935998736	0.0589906215459	0.138899584167	-0.0176383179549	0.228557931772	19.4001176328	8.03341328638	1.3273005047
17	2.41464506639	0.0145855051216	-0.138915947723	2.03547273057	-1.62155724292	3.30577331185	-0.0684066875525	-0.184990273419	-0.142264957826	0.0616812589406	-0.139211878748	-0.302631985903	0.0430947503461	0.423055842672	0.183027540532	0.145302274689	0.0227188051318	-0.00646301997559	0.163375162107	0.0274459586325	0.196331794205	17.7000649212	7.6480595121	20.6123490177
18	1.53582490196	0.579744927098	0.244411707645	1.53700352806	-0.0838571433152	7.28463105854	-0.0471268273228	0.251330631769	-0.0550127522026	-0.394896374175	0.0624509020327	0.0241738057531	0.436360859055	-0.134061405552	0.00339354904019	0.227633315485	-0.00106405848868	-0.0129617197726	0.142386469823	-0.0274127265807	0.150938222365	1.60550500242	5.01976220883	3.6336128195
19	9.56391881446	3.75258236812	0.570183153016	6.34177749423	-0.00313440687954	4.76829230938	-0.309304864006	0.546853523747	0.088403319164	-0.518381529966	0.322691674564	0.0889650335975	-0.199540132774	0.025432083873	0.0059806565163	0.321573851197	-0.0328859933759	0.0376157973779	0.206238340568	0.00173059504996	0.140134440343	17.5615400196	20.0381387161	-10.1091698774

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 53 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 54 through 80 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 81 through 95 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 96 through 121 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 122 through 151 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 152 through 166 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 167 through 178 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 179 through 207 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 208 through 227 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid -2 through 14 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 15 through 36 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 37 through 53 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 54 through 109 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 110 through 121 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 122 through 151 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 152 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 )

-
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