PDB-8ecp: R16A PA0709 with BME modifications

ID or keywords:

Entry

Database: PDB / ID: 8ecp

Title

R16A PA0709 with BME modifications

Components

Antibiotic biosynthesis monooxygenase

Keywords

CYTOSOLIC PROTEIN / glyoxal

Function / homology

Function and homology information

Oxidoreductases / monooxygenase activity / cytosol
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Cuthbert, B.J. / Goulding, C.W. / Ulijasz, A.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Structural characterization of PA0709
Authors: Cuthbert, B.J. / Goulding, C.W. / Ulijasz, A.T.

History

Deposition	Sep 2, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 27, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ecp.cif.gz	124.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8ecp.ent.gz	80.4 KB	Display	PDB format
PDBx/mmJSON format	8ecp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ecp_validation.pdf.gz	454.6 KB	Display	wwPDB validaton report
Full document	8ecp_full_validation.pdf.gz	455.8 KB	Display
Data in XML	8ecp_validation.xml.gz	13.6 KB	Display
Data in CIF	8ecp_validation.cif.gz	19.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ec/8ecp ftp://data.pdbj.org/pub/pdb/validation_reports/ec/8ecp	HTTPS FTP

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Related structure data

Related structure data	8ecxC 8eifC C: citing same article (ref.)
Similar structure data	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

Deposited unit

A: Antibiotic biosynthesis monooxygenase

B: Antibiotic biosynthesis monooxygenase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, dimer in solution, but hexameric crystal assembly

Unit cell

Length a, b, c (Å)	62.783, 62.783, 120.367
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3
Space group name Hall	R3
Symmetry operation	#1: x,y,z #2: -y,x-y,z #3: -x+y,-x,z #4: x+1/3,y+2/3,z+2/3 #5: -y+1/3,x-y+2/3,z+2/3 #6: -x+y+1/3,-x+2/3,z+2/3 #7: x+2/3,y+1/3,z+1/3 #8: -y+2/3,x-y+1/3,z+1/3 #9: -x+y+2/3,-x+1/3,z+1/3

Components on special symmetry positions

ID	Model	Components
1	1	A-201- ACT
2	1	A-205- ACT
3	1	B-203- ACT
4	1	B-203- ACT
5	1	A-386- HOH
6	1	A-414- HOH
7	1	A-428- HOH
8	1	B-301- HOH

#1: Protein	Antibiotic biosynthesis monooxygenase / Quinol monooxygenase YgiN Mass: 11754.042 Da / Num. of mol.: 2 / Mutation: R16A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A072ZNL3
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	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: 1.94 Å³/Da / Density % sol: 36.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium cacodylate pH 6.5, 0.2 M magnesium acetate, 30 % PEG 8000 Temp details: room temperature

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: cryo / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2022
Radiation	Monochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.5→31.39 Å / Num. obs: 28306 / % possible obs: 99.6 % / Redundancy: 5.7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.05 / R_pim(I) all: 0.035 / R_rim(I) all: 0.061 / Χ²: 0.77 / Net I/σ(I): 16.3
Reflection shell	Resolution: 1.5→1.52 Å / Redundancy: 5.4 % / R_merge(I) obs: 0.364 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1350 / CC_1/2: 0.875 / R_pim(I) all: 0.264 / R_rim(I) all: 0.451 / Χ²: 0.52 / % possible all: 96.4

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: unpublished

Resolution: 1.5→31.39 Å / SU ML: 0.1664 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 20.8059
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2047	2825	9.98 %
R_work	0.1758	25479	-
obs	0.1788	28304	99.61 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 23 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→31.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1589	0	73	253	1915

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	1713
X-RAY DIFFRACTION	f_angle_d	0.9142	2302
X-RAY DIFFRACTION	f_chiral_restr	0.0828	230
X-RAY DIFFRACTION	f_plane_restr	0.0052	313
X-RAY DIFFRACTION	f_dihedral_angle_d	11.6233	243

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 (%)
1.5-1.52	0.2938	137	0.2396	1219	X-RAY DIFFRACTION	96.38
1.52-1.55	0.2519	140	0.2319	1282	X-RAY DIFFRACTION	99.58
1.55-1.58	0.2613	145	0.2043	1277	X-RAY DIFFRACTION	99.51
1.58-1.61	0.2502	141	0.2026	1245	X-RAY DIFFRACTION	99.35
1.61-1.65	0.2286	143	0.1995	1310	X-RAY DIFFRACTION	99.86
1.65-1.69	0.2547	138	0.1898	1278	X-RAY DIFFRACTION	100
1.69-1.73	0.2329	139	0.187	1274	X-RAY DIFFRACTION	100
1.73-1.78	0.2282	137	0.1903	1251	X-RAY DIFFRACTION	99.93
1.78-1.83	0.2261	148	0.1936	1296	X-RAY DIFFRACTION	99.86
1.83-1.89	0.2452	142	0.1823	1280	X-RAY DIFFRACTION	99.79
1.89-1.96	0.2203	139	0.1743	1278	X-RAY DIFFRACTION	99.86
1.96-2.03	0.1858	142	0.1685	1260	X-RAY DIFFRACTION	99.36
2.03-2.13	0.2125	140	0.1682	1277	X-RAY DIFFRACTION	99.93
2.13-2.24	0.1853	146	0.1754	1280	X-RAY DIFFRACTION	100
2.24-2.38	0.1877	138	0.1689	1280	X-RAY DIFFRACTION	100
2.38-2.56	0.2263	144	0.1885	1287	X-RAY DIFFRACTION	100
2.56-2.82	0.2099	139	0.186	1270	X-RAY DIFFRACTION	99.51
2.82-3.23	0.1941	140	0.1741	1274	X-RAY DIFFRACTION	99.72
3.23-4.06	0.1825	139	0.1582	1281	X-RAY DIFFRACTION	99.93
4.07-31.39	0.181	148	0.1599	1280	X-RAY DIFFRACTION	99.65

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	4.37856170001	-0.606541419204	-3.18612293937	1.11125390893	0.531679577361	4.58940190389	0.12441288657	0.0810342854974	0.231353374461	-0.112873270117	0.0666482996371	0.0193328632024	-0.154430431337	-0.199374318111	-0.207666001152	0.103437166396	0.0191252531358	0.0119565064557	0.0949902854578	0.0353023560769	0.10721647753	-10.7683243642	-28.2648173927	10.0727936108
2	8.29978858265	-0.674727134551	-3.90354859179	2.12532381389	0.617946348309	4.68489373097	0.254966920041	0.14486385169	0.278999032137	-0.332609293513	-0.0549265463315	0.0802257831597	-0.10357346683	-0.2259003932	-0.194696709527	0.212585311444	0.0443810776018	0.0195459755987	0.203588850434	0.132291670386	0.176951308069	-13.4660886529	-21.8743354556	-0.758119798207
3	3.5953511869	-0.489796117669	-0.51963054761	1.54181002375	0.353191103562	1.63997548529	0.0670137929976	0.118178112607	0.286779041013	-0.00279336761737	0.12204176714	0.107341886626	-0.177494708969	-0.149017830612	-0.189433931981	0.138689881849	0.0259610180475	0.035905965216	0.100682960385	0.0416754412152	0.136625507801	-10.2669729107	-22.7450639369	8.65513457493
4	5.64014093722	1.84554087883	0.942057888757	2.23655147953	0.0584539467976	8.37269970109	0.0951648074431	0.0252686165773	-0.140017473811	-0.0375116173457	0.127419724199	0.36526478679	0.29615851151	-0.713789699346	-0.151153513199	0.106234710849	-0.00816141245241	-0.00966545262665	0.245179137346	0.0724386063767	0.241548264934	-24.6424666713	-29.7783956152	11.2307914306
5	5.23396423009	-0.521082089165	-1.48850505938	1.34203238684	0.351341362462	1.91990741515	0.118591583323	0.530058488279	0.0565872008899	-0.353017742535	0.099017036952	0.215969967926	0.216149330643	-0.643410291635	-0.204697272761	0.182442108891	-0.0168168347831	-0.013498043734	0.255065230284	0.076755382542	0.142413983733	-15.0975068297	-30.8598454755	-2.01748905056
6	2.11354974	-0.905587205447	-1.17840930417	3.38075004433	2.48477510049	3.84707989194	0.107103697926	-0.117304204416	0.160244808083	0.0172268888691	-0.0664575625161	0.273749253859	-0.1959321229	-0.105784335689	-0.0654861893243	0.119480102759	0.0052024325101	0.0354715943278	0.121802507939	0.0186424266791	0.121026484249	-14.7795901905	-26.0016746268	20.4824275324
7	1.0492368407	0.4345256674	-0.205728540161	3.63365029899	-2.58747713756	3.37807552581	0.121782926032	-0.147777866273	0.263228092417	-0.0403625559712	0.146526958548	0.0781380004374	-0.115804335167	-0.02286569411	-0.237974628131	0.130433337778	-0.00207555075455	0.0650584172673	0.133726998958	-0.0256319165045	0.158361957377	-4.00507023922	-23.4489352576	21.2179637159
8	1.65622347909	-0.581618798274	0.315592579803	6.15799779532	-1.24465621308	2.22511590438	0.320196487285	-0.497963064977	0.337443550705	0.154914867259	0.133037380278	0.0933735552074	-0.148554571263	0.0192859116854	-0.254481867541	0.14650075406	0.00533468297572	0.176969599542	0.265900869998	-0.109036618264	0.211884872406	-8.90063041201	-19.5563532371	32.2352296665
9	1.34948150327	1.28307280189	0.331687036079	4.8428054341	0.353107042483	0.120073041014	0.328884899384	-0.0938801616708	0.423448474124	0.258365219867	0.0490853901291	0.255081345462	-0.319420672976	0.130209782449	-0.263683821849	0.230272811354	-0.00386138328162	0.17065046087	0.149194959331	-0.0365749865827	0.221502842519	-9.19468025243	-15.5166534637	22.5310024579
10	5.29503238682	-2.67490129354	2.52993242918	3.0804587844	-3.01354953249	5.05125420676	0.405372498333	-0.282699949796	-0.430740777153	0.322219751373	-0.0208156966128	0.0834230547528	0.428519975506	-0.236860875588	-0.311281362003	0.202541450007	-0.0237849475898	-0.0040899966707	0.103879968639	0.0321555703129	0.155188830178	-12.8142411715	-35.3723909424	26.7160077687
11	0.545431396327	0.728276360669	-0.000588019928516	6.49179269382	-2.73557093845	1.89771992936	0.124194335331	-0.13522663927	0.228420748241	-0.131337084128	0.0174069673246	0.00897499887706	-0.109356116707	0.0523233577866	-0.140042369579	0.133102438943	0.000246265861091	0.0625034851364	0.134088628211	-0.0202009969839	0.138866604512	-6.93654782726	-22.1497726131	21.8235160913
12	3.27972405498	0.986550483874	0.322416399496	2.40340837991	0.00754079013602	6.5161163404	0.138603170616	-0.319914439233	0.631310680707	-0.109013630559	0.079580311659	-0.627170359707	-0.302427421521	0.698712704119	-0.18587893538	0.281377844314	-0.0863336088346	0.188799307584	0.250583498564	-0.128530633906	0.401845605989	2.67338106916	-11.0297361165	20.5753632803
13	4.82365551685	-0.0640702941544	-1.46493011894	2.01227864734	-4.80070508221	5.48871261338	0.055989441992	-0.545254579473	0.420947697003	0.302647081775	0.0162670883156	-0.581220570283	-0.28067638363	0.395160644582	-0.0793519488638	0.187899553037	-0.0509265214135	0.069952553731	0.303705009499	-0.125949363598	0.246537420413	-0.258561443221	-16.9966956085	33.600412845
14	3.14961934214	-0.783813725	-2.18489694624	4.74977978107	-1.49828007632	2.00515841247	0.175136497048	-0.545339352472	0.151054613359	0.495940101218	0.126504285561	-0.236787204274	-0.341236915031	0.261459051872	-0.267884854189	0.192337516714	-0.00552751894813	0.0130444574062	0.251801471877	-0.0109977124209	0.153335599859	0.504456978979	-27.6958543303	33.1659131745
15	2.27248569083	0.489264719883	0.4905874486	4.54138532785	-3.22406573916	8.38494198405	-0.0277409067869	-0.00998689213756	0.314144777866	-0.148368925339	0.179871641747	-0.00378752876972	-0.343303360386	-0.220296550964	-0.155059850419	0.162112316058	0.0273201447527	0.0733554176719	0.115285117191	0.00356571735848	0.170439777994	-3.1478949258	-19.9468593384	12.2084461883

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 2 through 12 )	A	A	2 - 12	1 - 11
2	2	chain 'A' and (resid 13 through 33 )	A	A	13 - 33	12 - 32
3	3	chain 'A' and (resid 34 through 58 )	A	A	34 - 58	33 - 57
4	4	chain 'A' and (resid 59 through 70 )	A	A	59 - 70	58 - 69
5	5	chain 'A' and (resid 71 through 87 )	A	A	71 - 87	70 - 86
6	6	chain 'A' and (resid 88 through 100 )	A	A	88 - 100	87 - 99
7	7	chain 'B' and (resid 2 through 12 )	B	K	2 - 12	1 - 11
8	8	chain 'B' and (resid 13 through 33 )	B	K	13 - 33	12 - 32
9	9	chain 'B' and (resid 34 through 44 )	B	K	34 - 44	33 - 43
10	10	chain 'B' and (resid 45 through 50 )	B	K	45 - 50	44 - 49
11	11	chain 'B' and (resid 51 through 58 )	B	K	51 - 58	50 - 57
12	12	chain 'B' and (resid 59 through 70 )	B	K	59 - 70	58 - 69
13	13	chain 'B' and (resid 71 through 80 )	B	K	71 - 80	70 - 79
14	14	chain 'B' and (resid 81 through 87 )	B	K	81 - 87	80 - 86
15	15	chain 'B' and (resid 88 through 97 )	B	K	88 - 97	87 - 96

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