PDB-7rj1: Crystal structure of Aro7p chorismate mutase from Candida albican...

ID or keywords:

Entry

Database: PDB / ID: 7rj1

Title

Crystal structure of Aro7p chorismate mutase from Candida albicans, complex with L-Trp

Components

Chorismate mutase

Keywords

TRANSFERASE / structural genomics / CSGID / center for structural genomics of infectious diseases / niaid / national institute of allergy and infectious diseases / CHORISMATE PYRUVATE MUTASE / ALLOSTERIC PROTEIN

Function / homology

Function and homology information

tryptophan binding / L-tyrosine binding / L-tyrosine biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / L-phenylalanine biosynthetic process / aromatic amino acid family biosynthetic process / metal ion binding / nucleus / cytoplasm
Similarity search - Function

Biological species

Candida albicans (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.16 Å

Authors

Stogios, P.J. / Evdokimova, E. / Tan, K. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of Aro7p chorismate mutase from Candida albicans, complex with L-Trp
Authors: Stogios, P.J.

History

Deposition	Jul 20, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 28, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 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

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Download

PDBx/mmCIF format	7rj1.cif.gz	511.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7rj1.ent.gz	375 KB	Display	PDB format
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Validation report

Summary document	7rj1_validation.pdf.gz	490.8 KB	Display	wwPDB validaton report
Full document	7rj1_full_validation.pdf.gz	503.3 KB	Display
Data in XML	7rj1_validation.xml.gz	42.8 KB	Display
Data in CIF	7rj1_validation.cif.gz	60.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rj/7rj1 ftp://data.pdbj.org/pub/pdb/validation_reports/rj/7rj1	HTTPS FTP

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Related structure data

Related structure data	5csmS S: Starting model for refinement
Similar structure data	7rj1-2 6f2g-d 2f9y-d 5bro-d 1hqv-3 2zn9-2 6a4b-3 6a47-d Search similar-shape structures by Omokage search (details) 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
Other databases	TargetTrack: CSGID-IDP98476

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#124 - Apr 2010 Concanavalin A and Circular Permutation similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Chorismate mutase

B: Chorismate mutase

C: Chorismate mutase

D: Chorismate mutase

hetero molecules

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

1

A: Chorismate mutase

B: Chorismate mutase

hetero molecules

defined by author&software
62.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Chorismate mutase

hetero molecules

D: Chorismate mutase

hetero molecules

defined by author&software
62.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.751, 93.154, 99.709
Angle α, β, γ (deg.)	90.000, 106.959, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Chorismate mutase Mass: 31102.691 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 / Gene: ARO7, orf19.1170, CAALFM_C111500CA / Plasmid: plasmid / Details (production host): BL21(DE3)-Gold / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -Gold / References: UniProt: Q59TS4, chorismate mutase

#1: Protein

Chorismate mutase

Mass: 31102.691 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: ARO7, orf19.1170, CAALFM_C111500CA / Plasmid: plasmid / Details (production host): BL21(DE3)-Gold / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -Gold / References: UniProt: Q59TS4, chorismate mutase

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Non-polymers , 5 types, 495 molecules

#2: Chemical	ChemComp-TRP / TRYPTOPHAN Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₂N₂O₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.19 Å³/Da / Density % sol: 43.88 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M magnesium chloride, 25% (w/v) PEG3350, 0.1 M Tris pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.15→50 Å / Num. obs: 56277 / % possible obs: 98 % / Redundancy: 3.3 % / B_iso Wilson estimate: 40.41 Å² / CC_1/2: 1 / R_merge(I) obs: 0.083 / R_pim(I) all: 0.053 / Net I/σ(I): 18.1
Reflection shell	Resolution: 2.15→2.19 Å / R_merge(I) obs: 0.701 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 2850 / CC_1/2: 0.882 / R_pim(I) all: 0.451 / % possible all: 98.8

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5csm

5csm

Resolution: 2.16→41.85 Å / SU ML: 0.2914 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5992
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2406	2008	3.57 %
R_work	0.1838	54227	-
obs	0.1858	56235	97.1 %

Solvent computation

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

Displacement parameters

B_iso mean: 58.6 Å²

Refinement step

Cycle: LAST / Resolution: 2.16→41.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8633	0	21	483	9137

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0034	8827
X-RAY DIFFRACTION	f_angle_d	0.6776	11939
X-RAY DIFFRACTION	f_chiral_restr	0.0462	1338
X-RAY DIFFRACTION	f_plane_restr	0.0048	1529
X-RAY DIFFRACTION	f_dihedral_angle_d	22.3276	3402

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 (%)
2.16-2.22	0.3508	128	0.2721	3446	X-RAY DIFFRACTION	86.5
2.22-2.27	0.3015	149	0.2488	3954	X-RAY DIFFRACTION	99.06
2.27-2.34	0.31	143	0.2365	3889	X-RAY DIFFRACTION	98.92
2.34-2.42	0.2836	153	0.22	3912	X-RAY DIFFRACTION	98.83
2.42-2.5	0.2877	137	0.2118	3905	X-RAY DIFFRACTION	98.25
2.5-2.6	0.265	139	0.201	3845	X-RAY DIFFRACTION	96.42
2.6-2.72	0.2766	148	0.2002	3906	X-RAY DIFFRACTION	98.09
2.72-2.87	0.2771	142	0.2065	3955	X-RAY DIFFRACTION	99.06
2.87-3.05	0.2625	147	0.1995	3922	X-RAY DIFFRACTION	98.86
3.05-3.28	0.2621	145	0.1944	3950	X-RAY DIFFRACTION	99.08
3.28-3.61	0.2438	139	0.1756	3864	X-RAY DIFFRACTION	96.46
3.61-4.13	0.1924	145	0.1474	3936	X-RAY DIFFRACTION	98.36
4.13-5.21	0.1859	144	0.1543	3835	X-RAY DIFFRACTION	95.67
5.21-41.85	0.2435	149	0.1823	3908	X-RAY DIFFRACTION	95.91

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	2.40126494357	0.101398021777	-0.635914417933	0.408837913365	0.72355059891	1.80629366545	0.108667915131	-0.164078777976	-0.0232033800595	0.0438007326908	-0.0854863043646	-0.130934856004	-0.183195292091	0.0297540977511	-0.0383171594901	0.321989645913	0.0461895209307	-0.0342039749206	0.246916889161	-0.030717203765	0.280067055377	19.6839422379	-4.05640201378	8.81231494978
2	2.07261980822	1.52507161675	0.0666750626198	6.29910479377	1.16208134851	0.435434859106	-0.015447792204	0.100428933518	-0.202681143121	-0.303037591258	-0.00716610744622	0.0798876580918	-0.0554430486749	-0.0242565375404	0.0374320108978	0.415294634686	0.0225860512224	0.0351092006938	0.293530334173	-0.0248587078406	0.416509810382	25.1011570206	-9.18601347245	-2.72795489755
3	5.1984627562	5.23932854997	4.85959014974	5.23839974599	4.88003480362	4.54724574548	-0.0850248541322	0.0615745556194	0.3580141045	-0.645504284022	0.124637726997	0.0142918114795	-0.487949178307	-0.0143238165169	-0.00471697107069	0.437223147218	0.0467087698304	0.0693362789159	0.297210983771	0.0271566523325	0.507705311641	12.4053768874	-2.36756529549	-0.254214688395
4	5.49715436119	3.2749351971	1.48746346887	6.58365639843	1.46666616987	1.26160563282	0.0639022152345	-0.0629550860503	0.0627345076953	0.363088898223	0.0639259086379	-0.212147354131	-0.0182405265807	0.0515713587338	-0.100101600232	0.322282900418	0.0310262303658	0.0710434742237	0.21119902095	0.0206587230385	0.239093804271	17.7048075893	-1.40155897265	8.58097742837
5	5.76010805181	1.62688101457	4.01585681269	1.15119950191	1.85759550711	5.79396901061	0.147105355415	-0.489894836159	-0.39665612284	0.143253053029	-0.0235175474637	0.286472140368	-0.0316999028601	-0.700842208964	-0.0785159455014	0.317559856146	0.0202471996361	0.0595706946803	0.297394035763	0.034822438405	0.525320894902	-0.430117278736	-11.1784207513	9.8109363265
6	7.00077601403	-1.06537379413	4.55805383473	3.42239453408	-1.17916107906	3.07718208864	-0.554827076382	-0.797279825115	0.852077437804	0.578158607933	-0.106000245427	0.0554036937574	-0.99530796237	-0.276276579526	0.650293092516	0.56883611811	-0.0541757301946	0.0928407032572	0.527496387739	-0.122044443998	0.57423474745	14.6783974988	3.05280266508	24.3247899567
7	5.43486573582	0.51985660353	1.55357973902	3.59289397921	1.47891320718	5.62137572189	0.184664002019	0.486577448833	-0.484402881951	-0.228844976155	-0.478593113158	0.380283544942	0.601639817954	-0.370396489117	0.233534478236	0.372568523655	0.0368463088103	0.0400981023448	0.279884892513	-0.0513591734045	0.502018587171	2.57992477297	-16.0002331139	-3.42059269163
8	1.6695301564	0.97852139273	-0.0634835829992	2.65991044177	-0.291486185662	2.04477528668	0.0728325321536	-0.134980904453	0.298518235083	0.0500480843204	-0.109453603983	-0.17491308506	-0.245142877932	0.278017332566	0.0168964634686	0.303574214794	-0.0179703226597	-0.00100668020157	0.289810303333	0.00749497072728	0.397453448422	38.9865441484	-0.284354290594	12.5556204379
9	7.31184804476	6.20508811984	0.992180782155	7.985985597	1.63557008629	2.86398767168	0.139996268837	-0.100156166313	-0.34369169502	0.0242041956453	-0.0948977643743	-0.367633115781	0.225318772162	0.199123065088	-0.0167992433832	0.326883515884	0.0693078737024	-0.00903439065449	0.325300015483	0.0392325825674	0.374264831693	41.0550330066	-12.5184434793	17.630411278
10	7.20214955728	7.5194870777	6.24390321775	9.07726320199	6.87745924388	5.55429115846	0.125368905107	-0.12181817121	0.333852656392	0.265775463088	-0.292715742026	0.254278855811	0.0536513806437	0.234822365353	0.211191466404	0.447207294507	-0.0821578773158	0.0236523259014	0.422136139208	0.00432488160092	0.39708714635	38.9729339301	-1.88582151725	18.3988760325
11	7.39264857975	3.66422330756	0.541106227457	3.75626185393	-0.452919824487	2.28295846692	0.132077344273	-1.42219659929	-0.348969775272	0.859209258588	-0.517133828519	-0.63074786175	-0.280897963473	0.637672697071	0.333172635569	0.714231419364	-0.160435087908	-0.099926428781	0.868581101542	-0.00278597123477	0.475727999163	45.3063564671	1.33010532699	34.8061202822
12	6.03424548675	-1.17992082837	-1.20516216283	1.46568303034	0.300873444495	3.41059164718	-0.268546827665	-0.41538205575	-1.58663020905	0.15491751535	0.0952531127245	0.228393475284	0.470473315922	-0.04230006812	0.210697979473	0.62140262378	-0.10866717639	-0.0109421478053	0.461449128855	0.126642584	0.568777519431	27.3802901495	-13.7699145731	29.5842416835
13	3.8468815715	0.350631929506	0.696017828491	3.66947477645	1.70574359314	1.26514071313	-0.0495268375802	-0.0157526863832	0.916948056436	0.197715116261	-0.155564589891	-0.296177072042	-0.766233853523	0.797050234911	0.0522952831563	0.588175286342	-0.302398579371	-0.16932816605	0.826691963325	0.00923322646947	0.687683997849	54.831875926	8.68324033053	25.8274488683
14	2.02072383167	-1.11793338664	-0.0123811330051	1.2439385022	0.294687876839	2.2875546468	0.113453242987	-0.808820508907	0.345197603707	0.322786397123	0.100233458835	0.155526086514	-0.327480964861	-0.0128246289807	-0.229420874369	0.540508289975	0.0569673940487	0.0837810504751	0.388706328428	-0.0721837582227	0.391213354344	19.5937759744	-42.4919877233	29.2073702468
15	4.09603111233	1.24510736795	1.48982685251	3.30189449212	1.0090700611	1.46666793099	-0.00110222787697	0.0425410558063	0.0970193375466	0.085616187025	-0.0347274470656	0.322674520025	-0.0426294392975	-0.117473470571	0.0434906452058	0.346472692486	0.0202010039497	0.0782149998987	0.297911178911	0.00722868844053	0.402310354675	18.404693259	-48.225684454	16.6271468327
16	4.19354371957	0.635040963	4.4879129897	1.5984458518	-0.0994831182533	5.29657758841	-0.321386157257	0.389411624578	1.06951339576	0.0899521910995	-0.0728356911661	-0.0386531640841	-0.0326150594904	0.0489423926676	0.366537483191	0.545146693501	0.0383753613199	0.201488807164	0.372962406413	-0.099539791636	0.612995802792	16.4498652655	-34.3850575862	21.3442691944
17	8.81356514766	-2.86117345851	1.92793791672	2.43458535382	-0.529870565494	0.880837672457	-0.254717942078	-0.278595762474	-0.317907824237	0.263031097368	0.342497723863	-0.145622919808	-0.269347570161	0.0502092888566	-0.0413807500585	0.539749362217	0.0248378031611	0.0977657832313	0.427230928258	-0.0508288533502	0.32598687845	20.1094556292	-39.3369220342	29.6514497664
18	5.2562064456	-2.00746988206	4.39097417513	2.22176374221	-1.71823200207	4.63549484041	-0.739034365681	-1.11508931518	0.218033604343	0.676529450489	0.699153678476	0.545860167081	-1.23065547542	-0.644430150433	0.0226895920791	0.720635631041	0.190324903193	0.19556278082	0.683476878174	-0.0821072938278	0.75681045913	1.23319034742	-30.7999591904	31.7814797275
19	3.90601606428	-1.05096964598	0.873421184479	3.44487148546	-4.81108058829	7.49768357887	-0.494002596273	-1.17484991651	0.329082896266	1.34854412135	0.140898423197	-1.17514827307	-1.4171756877	-0.477064650494	0.270269792092	0.86612589231	0.0724184784125	-0.0446979087628	0.694923408047	-0.22640719101	0.618217134672	20.6952620384	-36.38568975	44.874436388
20	3.14722191366	1.20449923606	1.80278651702	3.6858822788	0.0171138286842	4.60965691909	-0.474769244985	-0.353191441638	0.584743868901	-0.44073238422	0.08930490492	0.594345447414	-0.430501251266	-0.553525262727	0.394992756085	0.472902510977	0.135022325956	0.0305355744606	0.451512517804	0.0138327864252	0.651357043618	-0.37951560817	-33.8118400319	18.0170186519
21	2.87965892022	-0.317846663581	0.242881866794	2.00505812602	0.823111018832	2.29029771772	-0.0325922839632	0.742578727062	-0.14919987141	-0.327451959433	0.0101110278575	0.0604318022878	-0.0462022446232	-0.215994133781	0.0107480758223	0.398563094506	-0.0262777424826	0.0632388332468	0.48767456252	-0.0232467065538	0.349765855458	0.874593001092	-12.5775947331	58.1560393685
22	6.37629666152	0.753884581362	1.74426536548	5.98807801602	0.777956757336	4.45126041118	-0.0620800989593	0.668823334008	0.331212731507	0.390060891545	-0.159976766009	0.842014685662	-0.217548691853	-0.781484768998	0.199127760139	0.449118652989	-0.0772900822359	0.0248217984089	0.74708333035	-0.102553715086	0.417486855101	-17.468929421	-19.0483914061	52.2820327627

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 0 through 56 )	A	A	0 - 56	1 - 57
2	2	chain 'A' and (resid 57 through 102 )	A	A	57 - 102	58 - 103
3	3	chain 'A' and (resid 103 through 122 )	A	A	103 - 122	104 - 123
4	4	chain 'A' and (resid 123 through 169 )	A	A	123 - 169	124 - 170
5	5	chain 'A' and (resid 170 through 209 )	A	A	170 - 209	171 - 210
6	6	chain 'A' and (resid 210 through 238 )	A	A	210 - 238	211 - 237
7	7	chain 'A' and (resid 239 through 301 )	A	A	239 - 301	238 - 266
8	8	chain 'B' and (resid 0 through 105 )	B	B	0 - 105	1 - 106
9	9	chain 'B' and (resid 106 through 134 )	B	B	106 - 134	107 - 135
10	10	chain 'B' and (resid 135 through 169 )	B	B	135 - 169	136 - 170
11	11	chain 'B' and (resid 170 through 211 )	B	B	170 - 211	171 - 212
12	12	chain 'B' and (resid 212 through 238 )	B	B	212 - 238	213 - 237
13	13	chain 'B' and (resid 239 through 301 )	B	B	239 - 301	238 - 266
14	14	chain 'C' and (resid 0 through 56 )	C	C	0 - 56	1 - 57
15	15	chain 'C' and (resid 57 through 102 )	C	C	57 - 102	58 - 103
16	16	chain 'C' and (resid 103 through 122 )	C	C	103 - 122	104 - 123
17	17	chain 'C' and (resid 123 through 169 )	C	C	123 - 169	124 - 170
18	18	chain 'C' and (resid 170 through 209 )	C	C	170 - 209	171 - 210
19	19	chain 'C' and (resid 210 through 238 )	C	C	210 - 238	211 - 235
20	20	chain 'C' and (resid 239 through 301 )	C	C	239 - 301	236 - 264
21	21	chain 'D' and (resid 0 through 238 )	D	D	0 - 238	1 - 233
22	22	chain 'D' and (resid 239 through 301 )	D	D	239 - 301	234 - 262

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