PDB-6rgs: Crystal Structure of Phenylalanine Ammonia Lyase (PAL) from Petro...

ID or keywords:

Entry

Database: PDB / ID: 6rgs

Title

Crystal Structure of Phenylalanine Ammonia Lyase (PAL) from Petroselinum crispum bound to cinnamate

Components

Phenylalanine ammonia-lyase 1

Keywords

LYASE /

complex / bioctalysis /

protein

Function / homology

Function and homology information

phenylalanine ammonia-lyase / cinnamic acid biosynthetic process /

phenylalanine ammonia-lyase activity / L-phenylalanine catabolic process /

amino acid binding / protein-containing complex /

cytoplasm
Similarity search - Function

Biological species

Petroselinum crispum (parsley)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.42001023643 Å

Authors

Brem, J. / Lang, P. / Bencze, C.-L. / Schofield, C.

Funding support

United Kingdom, 1items

Citation

Journal: Acs Catalysis / Year: 2019
Title: Mapping the Hydrophobic Substrate Binding Site of Phenylalanine Ammonia Lyase from Petroselinum crispum
Authors: Nagy, E.Z.A. / Tork, S.D. / Lang, P.A. / Filip, A. / Irimie, F.D. / Poppe, L. / Tosa, M.I. / Schofield, C.J. / Brem, J. / Paizs, C. / Bencze, L.C.

History

Deposition	Apr 17, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 4, 2019	Provider: repository / Type: Initial release
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1	Jan 24, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6rgs.cif.gz	806.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6rgs.ent.gz	561.1 KB	Display	PDB format
PDBx/mmJSON format	6rgs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	1w27S S: Starting model for refinement
Similar structure data	3a9c-d 3tvw-1 4asi-2 3ff6-2 1t6p-2 2r7m-1 3tv5-1 1t6p-1 Search similar-shape structures by Omokage search (details) 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	#127 - Jul 2010 Crystallins similarity (2) #154 - Oct 2012 Citric Acid Cycle similarity (2)

Deposited unit

A: Phenylalanine ammonia-lyase 1

B: Phenylalanine ammonia-lyase 1

hetero molecules

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

1

A: Phenylalanine ammonia-lyase 1

B: Phenylalanine ammonia-lyase 1

hetero molecules

A: Phenylalanine ammonia-lyase 1

B: Phenylalanine ammonia-lyase 1

hetero molecules

defined by author&software
Evidence: gel filtration, tetramer, but dimer in the protein crystal structure
324 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	119.910, 159.820, 142.720
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

#1: Protein	Phenylalanine ammonia-lyase 1 / Mass: 80985.945 Da / Num. of mol.: 2 / Mutation: C704S, C716S, I460V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Petroselinum crispum (parsley) / Gene: PAL1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P24481, phenylalanine ammonia-lyase
#2: Chemical	ChemComp-K3Z / (E)-3-(4-methoxyphenyl)acrylic acid Mass: 178.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₀O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.63 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.2 M Ammonium acetate 20% w/v Polyethylene glycol 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 1, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 2.41→69.75 Å / Num. obs: 53282 / % possible obs: 100 % / Redundancy: 13 % / B_iso Wilson estimate: 45.8908257984 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.166 / R_pim(I) all: 0.048 / R_rim(I) all: 0.173 / Net I/σ(I): 11.6
Reflection shell	Resolution: 2.41→2.45 Å / Num. unique obs: 2638 / CC_1/2: 0.776 / R_pim(I) all: 0.529 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
SCALEPACK		data scaling
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1W27

1w27

Resolution: 2.42001023643→57.31 Å / SU ML: 0.295164738543 / Cross valid method: FREE R-VALUE / σ(F): 1.34361291239 / Phase error: 28.6282040409

	R_factor	Num. reflection	% reflection
R_free	0.238355287603	2675	5.11169287803 %
R_work	0.210293176916	-	-
obs	0.211769562404	52331	99.7236832076 %

Solvent computation

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

Displacement parameters

B_iso mean: 63.4249792115 Å²

Refinement step

Cycle: LAST / Resolution: 2.42001023643→57.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9333	0	0	81	9414

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00369895609033	9498
X-RAY DIFFRACTION	f_angle_d	0.58619910151	12896
X-RAY DIFFRACTION	f_chiral_restr	0.0380865903658	1513
X-RAY DIFFRACTION	f_plane_restr	0.00299748759111	1676
X-RAY DIFFRACTION	f_dihedral_angle_d	12.7775609831	5704

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 (%)
2.42-2.464	0.339732297372	125	0.30884144625	2554	X-RAY DIFFRACTION	99.7022701898
2.464-2.5114	0.314061294873	145	0.289933108374	2600	X-RAY DIFFRACTION	99.6370235935
2.5114-2.5627	0.298183587748	130	0.288779510337	2601	X-RAY DIFFRACTION	99.6351696461
2.5627-2.6184	0.328857308659	140	0.293479284316	2577	X-RAY DIFFRACTION	99.7430249633
2.6184-2.6793	0.313176891486	129	0.29576941391	2595	X-RAY DIFFRACTION	99.5978062157
2.6793-2.7463	0.305383046867	156	0.277398500899	2567	X-RAY DIFFRACTION	99.7801392451
2.7463-2.8206	0.304582673425	119	0.255392001147	2607	X-RAY DIFFRACTION	99.7438712038
2.8206-2.9036	0.278888729409	132	0.251840723674	2607	X-RAY DIFFRACTION	99.672489083
2.9036-2.9973	0.308327556934	131	0.263763745379	2609	X-RAY DIFFRACTION	99.8178506375
2.9973-3.1044	0.294346334475	128	0.246133436192	2613	X-RAY DIFFRACTION	99.7089850855
3.1044-3.2287	0.289476852024	138	0.235734502762	2619	X-RAY DIFFRACTION	99.782844734
3.2287-3.3757	0.262248326979	164	0.225996276805	2546	X-RAY DIFFRACTION	99.8526160648
3.3757-3.5536	0.292140856433	135	0.229470180562	2649	X-RAY DIFFRACTION	99.6420901933
3.5536-3.7763	0.272734035635	138	0.210656502382	2603	X-RAY DIFFRACTION	99.4918330309
3.7763-4.0678	0.225598967077	137	0.179816328563	2608	X-RAY DIFFRACTION	99.4565217391
4.0678-4.4771	0.156213375106	150	0.158996245398	2635	X-RAY DIFFRACTION	99.9641062455
4.4771-5.1248	0.184986376348	154	0.155016865555	2643	X-RAY DIFFRACTION	99.9642601858
5.1248-6.4559	0.200674711758	175	0.199335071545	2649	X-RAY DIFFRACTION	100
6.4559-69.7536	0.202942802685	149	0.181181850207	2774	X-RAY DIFFRACTION	99.6250852079

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	0.685821328642	0.78537401894	-0.340100103606	0.833845700037	0.0936149148801	0.889908991936	-0.137807572541	-0.146425432832	-0.48004083778	0.353286209091	0.103370766238	-0.0679084667928	0.259220918382	0.236689246109	0.027367874216	0.581285688546	0.0744151150873	0.049668499128	0.650118591734	0.156516836527	0.554565797154	-51.9745676993	-70.3196065052	61.5610737788
2	0.554665900042	0.0166995358948	-0.338810345311	0.356792562777	-0.179116833817	0.080443509054	-0.0275076233514	-0.141759630634	-0.293246493778	-0.0992325517931	-0.0776929916524	-0.427898427485	0.0878962757913	0.195618351772	0.0934448806838	0.489890286591	-0.0435756738374	0.0224831998953	0.569304951348	0.0481651730156	0.736928765903	-26.9564192967	-43.437356866	33.2992547331
3	0.982216951132	0.491316270312	-0.175834161562	0.954061511766	0.588533447055	1.1753874658	-0.140471018238	0.14432607353	-0.0900978895926	-0.103276479257	0.115624855879	-0.247330470487	0.155055678295	0.16121276286	0.0274513263056	0.501654988764	0.0238915673722	0.115291775413	0.541690345884	-0.00819069019841	0.56831380416	-33.5917643723	-58.8690560667	18.38552537
4	0.501391001569	-0.229440104301	-0.0988139386022	0.936813074039	0.483433358783	0.87929524459	-0.112162541939	0.0933371088303	-0.0271044855078	-0.224324525931	-0.0117520239627	-0.0695106703467	0.108154528518	0.0373086549755	0.107216762027	0.489694617112	-0.00853186725565	0.0984053609548	0.527403061912	0.028887173411	0.515769555696	-39.2531551183	-51.8528320717	17.4875692045
5	1.79775959479	-0.213556876628	0.387438464767	1.1100425134	0.138937408344	0.864675292262	-0.116014346523	-0.112424321734	0.442194453053	0.224238537615	0.0246705292231	-0.472444970201	-0.174828334444	0.232905672163	0.0479967594834	0.409769685851	-0.0253171102172	-0.0887121603788	0.512033606715	-0.0205812226131	0.631825175051	-38.1157821102	-18.9490232071	42.3323968287
6	0.274142092863	-0.320070350538	-0.0232473107729	0.212004441877	0.0935027224652	0.615464503678	-0.135330117958	-0.0870678460487	-0.0866454048793	0.139497187915	0.0596394291449	-0.22102422834	0.0970493200172	0.225021985234	0.0862272285026	0.444065901472	0.0655015924171	0.0170623234891	0.567113646886	0.0380572340832	0.560945039507	-35.9283661904	-52.5176876859	35.4926193654
7	0.1991844352	-0.723264083627	-0.0587855835054	1.48536942015	-0.0235789456616	0.259827325146	-0.14174659322	-0.0332106590292	-0.0544812958778	-0.0491656158687	0.284521022017	0.0631362202916	-0.123323392632	-0.0863129422791	-0.0997858167013	0.444563236444	-0.0147960397388	-0.0714509043262	0.479148765088	0.00639447669116	0.534872959281	-50.7497636035	-21.561481124	28.8611737844
8	0.762816195878	0.00777087292535	-0.35376019118	1.37707771401	-0.0453508348725	0.367694398114	-0.0967696821862	0.161718562764	0.0258759777642	-0.217520682991	0.118283139118	-0.236474781063	0.0429551014245	0.00915037910062	-0.0182990800335	0.396765437443	0.00448456502271	-0.0475042440479	0.462539013013	0.00638231228546	0.393404344421	-48.9160753344	-26.8023524582	26.9194038605
9	1.76090335668	0.0269339130975	0.0382057461144	1.22724600659	0.256116954505	2.08257300954	-0.345599953904	-0.00572457128067	0.555883338628	0.263871064896	-0.00552866951778	0.520158911173	0.120186071259	-0.0228973829944	0.272347953356	0.639709881785	0.0342072666419	0.0194582217612	0.606015221514	0.112407526996	0.949997608584	-49.9007202709	8.9341797348	29.5638265994
10	0.570718871211	0.208585951749	-0.296609519418	1.50100581982	-0.0299783072137	0.555031073676	-0.0128835426603	0.0638829658886	0.24679388156	-0.264793900197	0.124925016555	-0.0857341067415	-0.0966882765458	0.028239339088	-0.118323312493	0.451161816147	-0.0214379429587	0.0146166454844	0.480095672848	0.0651163955879	0.58032141782	-41.9470998788	-5.80469108477	23.032208424
11	0.491987279755	-0.000810660539929	0.442963371971	1.05770780643	0.0533617985155	0.276272802225	-0.00619978303157	-0.163137730676	-0.193191874401	0.342495531348	-0.0738306725051	-0.460332380549	-0.0123789037468	0.192888225089	0.0810073692567	0.486415174471	0.0647867288673	-0.112896711044	0.585260267338	0.025187639598	0.622387674837	-35.4645415309	-41.2541758405	58.0275632377
12	1.42026205619	-0.862926921909	0.0893662229634	0.805827378463	0.252167530402	0.792790740877	-0.187558718719	-0.339021126623	0.302383363101	0.328150965747	0.134276795508	-0.0743672791296	-0.108299330214	0.0518242335952	0.000485731049383	0.589212970722	0.0434286840162	-0.102864813564	0.567198229235	-0.0494170889902	0.37633881166	-50.065651654	-25.9781515074	65.5300237031
13	0.49836248634	-0.059079474029	-0.477444955538	0.625653272944	0.123247295639	0.814506605948	-0.0268019041282	-0.227132902199	0.0886362188094	0.316361393521	0.0249161825848	-0.172641871013	-0.105117642989	0.105140189779	0.0328584107608	0.50868388062	0.0309122102205	-0.0841896661488	0.611197198825	-0.0349729640279	0.411086521584	-54.9476093688	-33.0157014623	62.839334621
14	1.95482244105	1.01357702179	-0.00819783436128	1.39844041111	-0.196649325198	1.09024078104	-0.184389178432	-0.0398035010209	-0.305993374313	0.0326599188233	0.0541132336668	-0.521246272923	0.0528013599593	0.1068308073	0.114073227674	0.451612981062	0.070552629354	0.0374361311371	0.574869477261	0.0906506102495	0.695069866675	-38.6655334693	-66.2959373788	44.3843428123
15	0.43129487855	-0.247572247228	-0.0418647675727	1.10195628009	-0.108246061463	0.452673714414	-0.11249812775	-0.0894470466565	-0.107226818957	0.123328337752	0.0538658294253	-0.0910439386099	0.0319490241325	0.0455218567854	0.0570192041893	0.427593818282	0.0460043539998	0.00808281033627	0.479673947953	0.0198526830346	0.443990294873	-52.930108848	-52.9544224427	49.0185394154
16	0.515216133834	-0.120176700253	0.400800932776	0.0285823657944	-0.0245998504271	0.910644943362	-0.28581654616	0.144465328883	-0.607238566869	0.145291543003	0.249986425528	0.140124582517	-0.0637890008163	-0.191733996059	0.0662763489416	0.970969976276	0.0160880667446	0.215544928466	0.54677415941	0.0647932253652	1.17138739033	-57.8890522422	-97.8532023927	45.6557968194

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 630 through 716 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 65 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 66 through 187 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 188 through 293 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 294 through 355 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 356 through 402 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 403 through 455 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 456 through 547 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 548 through 587 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 588 through 715 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 25 through 65 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 66 through 187 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 188 through 293 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 294 through 355 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 356 through 547 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 548 through 629 )

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-Aug 12, 2020. Covid-19 info

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+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