PDB-9rsb: Crystal Structure of Phenylalanine Ammonia Lyase (PAL) from Petro...

ID or keywords:

Entry

Database: PDB / ID: 9rsb

Title

Crystal Structure of Phenylalanine Ammonia Lyase (PAL) from Petroselinum crispum bound to N-Phenylglycine

Components

Phenylalanine ammonia-lyase 1

Keywords

LYASE / biocatalysis / bioisostere inhibitor / induced fit

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: 1.9 Å

Authors

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

Funding support

United Kingdom, European Union,

Romania, 3items

Organization	Grant number	Country
Medical Research Council (MRC, United Kingdom)	MRF-145-0004-TPG-AVISO	United Kingdom
European Union (EU)	760251./28.12.2023	European Union
National Authority for Scientific Research in Romania (ANCS)	PNRR-C9-I8-CF92/31.07.2023	Romania

Citation

Journal: To Be Published
Title: Crystal Structure of Phenylalanine Ammonia Lyase (PAL) from Petroselinum crispum bound to N-Phenylglycine
Authors: Lang, P.A. / Schofield, C.J. / Bencze, L.C. / Brem, J.

History

Deposition	Jun 30, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 8, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9rsb.cif.gz	548.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9rsb.ent.gz		Display	PDB format
PDBx/mmJSON format	9rsb.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/rs/9rsb ftp://data.pdbj.org/pub/pdb/validation_reports/rs/9rsb	HTTPS FTP

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Related structure data

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

Unit cell

Length a, b, c (Å)	120.315, 162.439, 143.525
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-1257- HOH
2	1	B-1230- HOH

#1: Protein	Phenylalanine ammonia-lyase 1 Mass: 80985.945 Da / Num. of mol.: 2 / Mutation: I460V, C704S, C714S 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-A1JJC / N-Phenylglycine / 2-phenylazanylethanoic acid Mass: 151.163 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₉NO₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 927 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.16 Å³/Da / Density % sol: 43.18 %
Crystal grow	Temperature: 278 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: 0.9762 Å

Detector

Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 7, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9762 Å / Relative weight: 1

Reflection

Resolution: 1.9→48.341 Å / Num. obs: 110331 / % possible obs: 100 % / Redundancy: 12.4 % / B_iso Wilson estimate: 27.32 Å² / CC_1/2: 1 / R_rim(I) all: 0.166 / Net I/σ(I): 11

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.9-1.93	12.8	1	5472	0.8	1.325	99.7
5.16-48.36	13.6	46.2	5797	1	0.047	100

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Processing

Software

Name	Version	Classification
PHENIX	1.14	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→48.341 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.8 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1925	5472	4.97 %
R_work	0.1619	-	-
obs	0.1634	110189	99.89 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→48.341 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10326	0	30	927	11283

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	10697
X-RAY DIFFRACTION	f_angle_d	0.663	14527
X-RAY DIFFRACTION	f_dihedral_angle_d	12.549	6496
X-RAY DIFFRACTION	f_chiral_restr	0.04	1676
X-RAY DIFFRACTION	f_plane_restr	0.004	1915

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 (%)
1.9002-1.9218	0.3384	179	0.3191	3412	X-RAY DIFFRACTION	99
1.9218-1.9444	0.303	179	0.3012	3490	X-RAY DIFFRACTION	100
1.9444-1.9681	0.302	190	0.2769	3452	X-RAY DIFFRACTION	100
1.9681-1.993	0.2733	180	0.2474	3468	X-RAY DIFFRACTION	100
1.993-2.0193	0.2635	186	0.2303	3458	X-RAY DIFFRACTION	100
2.0193-2.0469	0.2312	158	0.2237	3451	X-RAY DIFFRACTION	100
2.0469-2.0762	0.2247	179	0.2073	3491	X-RAY DIFFRACTION	100
2.0762-2.1072	0.2189	165	0.1952	3501	X-RAY DIFFRACTION	100
2.1072-2.1401	0.1974	175	0.1927	3461	X-RAY DIFFRACTION	100
2.1401-2.1752	0.2127	183	0.1849	3448	X-RAY DIFFRACTION	100
2.1752-2.2127	0.218	164	0.1767	3460	X-RAY DIFFRACTION	100
2.2127-2.2529	0.2077	172	0.1785	3487	X-RAY DIFFRACTION	100
2.2529-2.2962	0.2029	197	0.1789	3467	X-RAY DIFFRACTION	100
2.2962-2.3431	0.2156	182	0.1699	3485	X-RAY DIFFRACTION	100
2.3431-2.3941	0.2219	176	0.1616	3462	X-RAY DIFFRACTION	100
2.3941-2.4498	0.1852	166	0.1606	3472	X-RAY DIFFRACTION	100
2.4498-2.511	0.2267	194	0.1593	3479	X-RAY DIFFRACTION	100
2.511-2.5789	0.2111	174	0.1567	3494	X-RAY DIFFRACTION	100
2.5789-2.6548	0.2057	198	0.1638	3453	X-RAY DIFFRACTION	100
2.6548-2.7405	0.2091	198	0.1587	3484	X-RAY DIFFRACTION	100
2.7405-2.8384	0.1927	172	0.1582	3489	X-RAY DIFFRACTION	100
2.8384-2.952	0.195	206	0.1682	3485	X-RAY DIFFRACTION	100
2.952-3.0864	0.1983	161	0.1646	3518	X-RAY DIFFRACTION	100
3.0864-3.2491	0.1968	194	0.1543	3508	X-RAY DIFFRACTION	100
3.2491-3.4526	0.2218	181	0.154	3495	X-RAY DIFFRACTION	100
3.4526-3.719	0.1889	183	0.1462	3513	X-RAY DIFFRACTION	100
3.719-4.0931	0.1429	178	0.1248	3556	X-RAY DIFFRACTION	100
4.0931-4.685	0.1394	220	0.1117	3501	X-RAY DIFFRACTION	100
4.685-5.9009	0.1405	179	0.1326	3597	X-RAY DIFFRACTION	100
5.9009-48.341	0.1776	203	0.1681	3680	X-RAY DIFFRACTION	100

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	0.6887	0.022	-0.055	0.9722	-0.2123	0.5884	-0.0499	0.1089	0.1487	-0.1831	0.0387	0.2593	-0.078	-0.1128	0.0094	0.2529	-0.0006	-0.0898	0.2776	0.0255	0.3183	-24.511	-21.7237	19.3391
2	1.0296	0.0703	-0.2404	1.4248	-0.4043	0.9688	-0.0534	-0.092	-0.2767	0.015	0.0333	0.3018	0.1561	-0.062	0.0075	0.1663	-0.0204	0.0162	0.2271	0.019	0.3027	-22.7012	-57.4876	35.7796
3	1.8304	-2.6396	1.0169	7.1851	-2.8616	1.7126	-0.086	-0.1156	-0.2678	-0.0221	0.1969	0.4245	0.1016	-0.0599	-0.1247	0.171	-0.0237	0.0309	0.2375	0.01	0.2336	-18.4953	-53.3197	39.209
4	0.4869	-0.0998	0.0727	1.996	0.1141	0.2352	-0.058	0.0234	-0.0822	-0.0861	0.0628	0.1513	0.0078	-0.0209	0.0003	0.129	-0.0137	0.0011	0.1814	-0.0019	0.1298	-12.3784	-50.2315	28.0592
5	1.9214	-1.6307	0.7926	3.7626	-0.6478	0.9777	0.1038	-0.071	-0.444	-0.1203	0.057	0.1973	0.214	-0.009	-0.1813	0.2664	-0.0553	-0.026	0.2698	-0.0435	0.5073	-12.4281	-90.7375	26.8279
6	3.0065	-0.5733	-1.1129	0.9293	0.7783	2.4944	-0.0706	0.2267	-0.2342	-0.1927	-0.0016	0.2682	0.0365	-0.2171	0.0932	0.2168	-0.0503	-0.0526	0.1988	-0.0141	0.3043	-21.8714	-59.5714	20.6222
7	0.0605	0.2814	-0.2188	1.4569	-1.3669	1.6311	-0.0087	0.1588	0.0109	-0.2399	-0.0952	-0.3083	0.1488	0.1589	0.1108	0.2714	-0.0259	0.1284	0.3404	-0.0301	0.311	25.3995	-39.1085	14.5442
8	1.2499	0.2899	-0.1462	1.0457	-0.2529	0.6013	-0.0401	0.2394	-0.21	-0.3326	0.0511	-0.1697	0.0947	0.0902	0.0018	0.3372	-0.0407	0.0688	0.308	-0.0925	0.2238	10.1592	-59.0086	9.8534
9	0.532	0.2261	0.1359	1.039	0.1022	0.2391	-0.0769	0.2454	-0.0674	-0.3829	0.0752	-0.0576	0.0428	0.0613	0.007	0.3247	-0.0393	0.0642	0.3204	-0.0245	0.1669	7.3122	-49.0528	7.5467
10	2.71	-0.4654	0.0728	1.1061	0.1625	1.8574	-0.0103	0.1429	0.5892	-0.0934	-0.0488	-0.3742	-0.2672	0.1366	0.0748	0.2307	-0.0623	-0.0034	0.2685	0.0355	0.3904	22.7322	-12.5987	26.5822
11	1.1626	-0.7949	-0.3535	5.4791	2.4347	1.8746	-0.0455	0.0123	0.217	-0.197	0.1421	-0.4957	-0.1576	0.1095	-0.1024	0.1857	-0.0373	0.0059	0.2898	0.0366	0.2449	17.1968	-22.8185	28.3247
12	0.5981	-0.2259	0.0786	1.9005	-0.0542	0.3102	-0.0696	0.0843	0.1357	-0.1311	0.0397	-0.1113	-0.0501	0.0215	0.0265	0.1766	-0.0327	-0.0024	0.2165	0.0132	0.1453	5.794	-25.9881	22.5841
13	0.6729	-0.6882	-0.3938	2.3629	0.8985	1.2053	-0.0883	0.062	0.4911	-0.1529	0.0545	-0.2012	-0.3011	0.0643	0.0045	0.3907	-0.0484	-0.1056	0.2837	0.1117	0.6427	5.5156	15.4754	21.5047
14	2.7559	-0.6521	0.3217	0.3095	-0.1512	0.8908	-0.1005	0.4299	0.26	-0.2034	-0.0137	-0.163	-0.0404	0.0863	0.1394	0.3276	-0.0531	0.0204	0.283	0.0777	0.2803	9.349	-16.4826	11.0147

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 25 through 260 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 261 through 336 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 337 through 377 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 378 through 545 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 546 through 663 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 664 through 714 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 25 through 65 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 66 through 169 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 170 through 291 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 292 through 336 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 337 through 377 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 378 through 545 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 546 through 663 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 664 through 714 )

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