PDB-7tdl: M379A mutant tyrosine phenol-lyase complexed with 3-bromo-DL-phen...

ID or keywords:

Entry

Database: PDB / ID: 7tdl

Title

M379A mutant tyrosine phenol-lyase complexed with 3-bromo-DL-phenylalanine

Components

Tyrosine phenol-lyase

Keywords

LYASE / pyridoxal-5'-phosphate / mutation / substrate specificity

Function / homology

Function and homology information

tyrosine phenol-lyase / tyrosine phenol-lyase activity / tyrosine metabolic process
Similarity search - Function

Biological species

Citrobacter freundii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Phillips, R.S.

Funding support

United States, 1items

Citation

Journal: Chembiochem / Year: 2022
Title: M379A Mutant Tyrosine Phenol-lyase from Citrobacter freundii Has Altered Conformational Dynamics.
Authors: Phillips, R.S. / Jones, B. / Nash, S.

History

Deposition	Jan 1, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 1, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jul 20, 2022	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 1.2	Aug 10, 2022	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7tdl.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb7tdl.ent.gz	911.2 KB	Display	PDB format
PDBx/mmJSON format	7tdl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7tdl_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	7tdl_full_validation.pdf.gz	1.9 MB	Display
Data in XML	7tdl_validation.xml.gz	79.8 KB	Display
Data in CIF	7tdl_validation.cif.gz	119.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/td/7tdl ftp://data.pdbj.org/pub/pdb/validation_reports/td/7tdl	HTTPS FTP

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Related structure data

Related structure data	7tcsC 2vlhS S: Starting model for refinement 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: Tyrosine phenol-lyase

B: Tyrosine phenol-lyase

C: Tyrosine phenol-lyase

D: Tyrosine phenol-lyase

hetero molecules

208 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	61.250, 82.870, 94.330
Angle α, β, γ (deg.)	113.160, 96.540, 102.210
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Tyrosine phenol-lyase / Beta-tyrosinase Mass: 51448.637 Da / Num. of mol.: 4 / Mutation: M379A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: tpl / Production host: Escherichia coli (E. coli) / References: UniProt: P31013, tyrosine phenol-lyase

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Non-polymers , 6 types, 1544 molecules

#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-OY3 / (4Z)-4-({[(1E)-2-(3-bromophenyl)-1-carboxyethylidene]azaniumyl}methylidene)-2-methyl-5-[(phosphonooxy)methyl]-1,4-dihydropyridin-3-olate Mass: 473.212 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₁₇H₁₈BrN₂O₇P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1528 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.03 Å³/Da / Density % sol: 39.5 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES, pH 7.5, 0.2 mM PLP, 1 mM DTT, 19% PEG 5000MME

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 27, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.6→58.41 Å / Num. obs: 213258 / % possible obs: 98.65 % / Redundancy: 7.6 % / B_iso Wilson estimate: 24.92 Å² / CC_1/2: 0.997 / Net I/σ(I): 6.48
Reflection shell	Resolution: 1.6→1.657 Å / Num. unique obs: 21321 / CC_1/2: 0.333

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
autoPROC	20211020	data processing
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2VLH

2vlh

Resolution: 1.6→58.41 Å / SU ML: 0.2452 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.778
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.221	1985	0.94 %
R_work	0.1774	209779	-
obs	0.1778	211764	98.65 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 35.33 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→58.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14481	0	79	1529	16089

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0137	15210
X-RAY DIFFRACTION	f_angle_d	1.2054	20561
X-RAY DIFFRACTION	f_chiral_restr	0.0651	2181
X-RAY DIFFRACTION	f_plane_restr	0.0127	2690
X-RAY DIFFRACTION	f_dihedral_angle_d	13.6438	5802

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 (%)
1.6-1.64	0.3573	134	0.3557	14213	X-RAY DIFFRACTION	93.39
1.64-1.68	0.3889	140	0.3337	14809	X-RAY DIFFRACTION	97.53
1.68-1.73	0.3296	141	0.3108	14823	X-RAY DIFFRACTION	97.86
1.73-1.79	0.2927	141	0.2864	14953	X-RAY DIFFRACTION	98.4
1.79-1.85	0.3577	141	0.266	14892	X-RAY DIFFRACTION	97.72
1.85-1.93	0.3007	144	0.2434	15143	X-RAY DIFFRACTION	99.75
1.93-2.02	0.2841	143	0.2295	15102	X-RAY DIFFRACTION	99.66
2.02-2.12	0.3055	143	0.214	15107	X-RAY DIFFRACTION	99.49
2.12-2.26	0.2446	143	0.1994	15128	X-RAY DIFFRACTION	99.34
2.26-2.43	0.2627	142	0.1914	15068	X-RAY DIFFRACTION	99.28
2.43-2.67	0.2219	143	0.1835	15087	X-RAY DIFFRACTION	99.42
2.67-3.06	0.2492	143	0.1683	15145	X-RAY DIFFRACTION	99.68
3.06-3.86	0.1759	143	0.1381	15143	X-RAY DIFFRACTION	99.78
3.86-58.41	0.1447	144	0.1264	15166	X-RAY DIFFRACTION	99.85

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	1.03170442771	-0.408001750006	-0.147239948861	1.38135713739	0.117437222137	1.29373427843	-0.0279304695882	-0.159526894634	-0.0666999664249	0.135071825651	-0.0160333673153	0.392651200646	-0.0520721904849	-0.320884142561	0.00211791107824	0.175302281908	0.0138335231062	0.0344641808051	0.29290478865	-0.00736527822646	0.306870982324	-26.0362149249	29.2779207987	-14.0571509722
2	0.651628322678	-0.0592953031385	0.284750724724	1.50052742847	-0.660086191169	0.795201654888	-0.0732264721127	-0.11005351958	0.11984067009	0.557441949353	0.00334167678794	-0.211936755024	-0.248729849587	0.0674561232262	0.0335948654791	0.32583693869	-0.00803441705736	-0.063811768402	0.236810754293	-0.0149623804197	0.246158487132	1.79788131724	33.7888679391	-6.90906004544
3	0.490387885263	0.0971890270217	0.19701671959	1.17799253247	0.4454639259	0.645913270255	0.0215637680366	0.0115244592704	0.0397678933459	0.107514643915	-0.00801180028575	-0.0863582030974	-0.071085922933	0.109027964835	0.00209402322822	0.201490906235	-0.0123465600588	-0.00595570532843	0.222995179923	0.0125739855625	0.22617921167	-1.55950858153	28.6354948701	-15.2226942175
4	0.720014844799	-0.111137723665	-0.0324969114828	0.614872578074	-0.676149905207	0.739689709714	-0.267488371664	-0.347958378909	0.492062893621	0.771967683756	0.298309291877	-0.135946196305	-0.298526530492	0.0338978862073	0.0768056686401	0.497183347199	0.117677422801	-0.067301026333	0.300497606363	-0.115690890494	0.352161313574	-21.0237696874	41.7498424822	-3.32179703926
5	0.748401322128	0.465695180217	0.115302346923	0.678253013668	-0.270039853126	1.01457296636	-0.531547907682	-0.523128332927	0.35901761623	0.928608201249	0.380095868321	0.516040080894	0.453339364776	0.0548542120797	-0.166589657807	0.773055922762	0.342107037721	0.177266577118	0.480934419365	-0.125879485746	0.282933576282	-28.0998688079	38.8386025442	-2.48885860007
6	0.926930162645	-0.462740401148	0.452955405676	0.968536606724	-0.29803493886	0.99554197322	-0.00683979964333	0.152552331185	0.0441351650891	-0.123636939281	-0.085145111266	-0.453956809063	0.152936500099	0.273393499543	0.07186098638	0.321546754589	0.048013911133	0.0332656551619	0.251645910048	0.0258561268211	0.369915135546	0.960403762342	-3.86436422688	-16.7490977865
7	0.774155039662	-0.000163602402776	0.100104499445	1.24775896751	-0.520938541478	0.844680193746	0.0248072795604	-0.290161609387	-0.0727335579748	0.534834379015	-0.0228545385292	0.0934855815042	0.0527083587825	-0.0170179606679	-0.0043285655022	0.510550435253	-0.0195117907324	0.04007213221	0.340754004803	0.0188281436679	0.211865929529	-12.6436472056	1.90115162727	7.85383187547
8	0.766329973591	0.0275817026137	0.0518840925358	0.583485999092	-0.423766325817	0.744334040626	0.0136387389084	-0.126818183074	-0.0531081643068	0.379925843422	0.051939792786	0.128804808769	0.0311626479265	-0.08479453136	-0.0167088171058	0.353014589643	-0.0139432099355	0.0244788581278	0.245418045181	0.0142562276456	0.205132527942	-13.9424099349	3.36881190563	-2.97579671233
9	1.28276882008	-0.321640869843	0.10474505028	0.977375776051	-0.672763548598	0.848718936942	-0.0994011091542	-0.136823364706	0.276060481825	0.246878171914	-0.132491550168	-0.700049713476	0.174704165896	0.399809740048	0.0732874467952	0.446501660027	0.063274301516	-0.122189329152	0.367735302154	0.0509494456736	0.572550194382	10.8637809399	-6.59762323523	-4.12584109696
10	0.281291966364	0.132651169065	0.161826774657	0.528035701505	-0.251058863393	1.27869528685	-0.0694422331026	0.130121840302	0.0599653874377	-0.134649117954	-0.0473123214146	-0.12851243093	-0.15057188802	0.20182732567	0.0438347332725	0.223994199388	-0.00253163524023	0.00426822348609	0.265020426149	0.0219592778878	0.29961429613	-18.1869231257	26.8705458399	-40.8239736977
11	0.56553409112	-0.05146851718	0.196310133818	0.391375943506	0.131036126371	0.618820755236	0.00986344400455	0.0142704351394	-0.0358670823489	-0.0490471642356	-0.0108473116738	0.0824960807838	0.025773141063	-0.123940235783	0.00676021648344	0.167595606881	-0.0109615904704	0.00190534050592	0.243695978882	-0.0041955302642	0.247202048976	-40.9189468414	13.3751129192	-41.1161987823
12	0.801984932777	-0.334043883928	0.0158487892176	0.905705511775	0.170054899323	0.884782305056	0.0104762018577	0.237081334933	0.0465628257359	-0.300073020532	-0.0541318345767	-0.058826969253	-0.200657140223	0.0087616614676	0.0229707266735	0.332098376437	0.00669793044648	-0.0145331281938	0.266132007275	0.0247606523451	0.270520983218	-26.7467261014	30.0908177679	-53.7633211926
13	1.00751718902	0.568677941302	0.429753577386	1.02886911478	0.25733647902	0.564125250208	0.123214763006	-0.142811489162	-0.0558494245977	0.312606978278	-0.111467764987	0.15470146915	0.249093793713	-0.122892114954	0.00285404113954	0.393287249446	-0.0207422345895	0.0265513914005	0.246239319988	0.0197714968851	0.305050140094	-23.3706973347	-12.9657589415	-25.4538051621
14	0.546863002173	-0.181192633679	0.140714284662	1.18445435952	0.365263542967	0.868227366856	0.0283441116618	0.109473811693	-0.0778322541285	-0.088035111613	0.00336577337018	-0.0575874786971	0.140510252927	0.0719152967419	-0.0178559085617	0.20469484527	0.0119808758178	0.00994336105194	0.213238781728	-0.00914797612623	0.204754425499	-11.7434379284	-7.0774517555	-48.3305412456
15	0.84395467649	-0.226169056483	-0.212285482468	0.871145222254	-0.0124345478113	0.508554665276	0.00474730409346	0.144573905389	-0.229980066538	-0.0896809594158	-0.00835338110611	0.214379203898	0.314302968038	-0.0951007132211	0.0182691180052	0.443225743181	-0.03403452715	-0.0293577892222	0.244616915564	-0.0219927009683	0.339973351347	-24.1529737535	-23.8756134129	-38.3588880721
16	0.84683137685	-0.163253012904	0.250401427371	0.547206986143	0.132747715406	0.460354944224	-0.061978447749	-0.0275122537791	-0.231803347922	0.240456907077	0.0445816432997	0.231987458142	0.201531945331	-0.193319401216	0.0281834248048	0.489260441086	-0.0520855757191	0.0115195776387	0.288700824886	-0.011800016004	0.397354772554	-29.5122961905	-23.4611466737	-33.0759206591

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 1 through 57 )	A	A	1 - 57	1 - 57
2	2	chain 'A' and (resid 58 through 228 )	A	A	58 - 228	58 - 228
3	3	chain 'A' and (resid 229 through 331 )	A	A	229 - 331	229 - 331
4	4	chain 'A' and (resid 332 through 413 )	A	A	332 - 413	332 - 413
5	5	chain 'A' and (resid 414 through 456 )	A	A	414 - 456	414 - 456
6	6	chain 'B' and (resid 1 through 57 )	B	F	1 - 57	1 - 57
7	7	chain 'B' and (resid 58 through 271 )	B	F	58 - 271	58 - 271
8	8	chain 'B' and (resid 272 through 332 )	B	F	272 - 332	272 - 332
9	9	chain 'B' and (resid 333 through 456 )	B	F	333 - 456	333 - 456
10	10	chain 'C' and (resid 1 through 57 )	C	J	1 - 57	1 - 57
11	11	chain 'C' and (resid 58 through 331 )	C	J	58 - 331	58 - 331
12	12	chain 'C' and (resid 332 through 456 )	C	J	332 - 456	332 - 456
13	13	chain 'D' and (resid 1 through 57 )	D	N	1 - 57	1 - 57
14	14	chain 'D' and (resid 58 through 331 )	D	N	58 - 331	58 - 331
15	15	chain 'D' and (resid 332 through 413 )	D	N	332 - 413	332 - 413
16	16	chain 'D' and (resid 414 through 456 )	D	N	414 - 456	414 - 456

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