PDB-3pph: Crystal structure of the Candida albicans methionine synthase by ...

ID or keywords:

Entry

Database: PDB / ID: 3pph

Title

Crystal structure of the Candida albicans methionine synthase by surface entropy reduction, threonine variant

Components

5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase

Keywords

TRANSFERASE / cobalamin-independent / Surface entropy reduction / Zn binding

Function / homology

Function and homology information

L-methionine biosynthetic process from homoserine via O-acetyl-L-homoserine and cystathionine / : /

5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase /

5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / fungal biofilm matrix / hyphal cell wall / adenine biosynthetic process / methionine metabolic process / 'de novo' L-methionine biosynthetic process / fungal-type cell wall ...
Similarity search - Function

Biological species

Candida albicans (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Ubhi, D. / Kavanagh, K. / Monzingo, A.F. / Robertus, J.D.

Citation

Journal: Arch.Biochem.Biophys. / Year: 2011
Title: Structure of Candida albicans methionine synthase determined by employing surface residue mutagenesis.
Authors: Ubhi, D. / Kavanagh, K.L. / Monzingo, A.F. / Robertus, J.D.

History

Deposition	Nov 24, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 12, 2011	Provider: repository / Type: Initial release
Revision 1.1	Sep 6, 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 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3pph.cif.gz	568.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3pph.ent.gz	465.3 KB	Display	PDB format
PDBx/mmJSON format	3pph.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/pp/3pph ftp://data.pdbj.org/pub/pdb/validation_reports/pp/3pph	HTTPS FTP

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Related structure data

Related structure data	3ppcSC 3ppfC 3ppgC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4l5z-d 3ppg-d 4l6h-d 3ppf-d 3ppc-1 5xe1-d 4pk6-d 4zty-d 4l61-d 5x2c-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase

B: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase

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

1

A: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase

defined by author&software
88.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase

defined by author&software
88.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	163.636, 98.080, 162.586
Angle α, β, γ (deg.)	90.00, 131.10, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain A and (resseq 1:102 or resseq 114:208 or resseq...
2	1	1	chain B and (resseq 1:102 or resseq 114:208 or resseq...

#1: Protein	5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase / Cobalamin-independent methionine synthase / Methionine synthase / vitamin-B12 independent isozyme Mass: 88279.031 Da / Num. of mol.: 2 / Mutation: K103T, K104T, E107T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Strain: BWP17 / Gene: CaO19.10083, CaO19.2551, MET6 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P82610, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase / Cobalamin-independent methionine synthase / Methionine synthase / vitamin-B12 independent isozyme

Mass: 88279.031 Da / Num. of mol.: 2 / Mutation: K103T, K104T, E107T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Candida albicans (yeast) / Strain: BWP17 / Gene: CaO19.10083, CaO19.2551, MET6 / Plasmid: pNIC28-Bsa4 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P82610,

5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.87 Å³/Da / Density % sol: 57.1 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 25% (w/v) PEG-MME 2000, 75 mM KSCN, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.3.1 / Wavelength: 1.11587 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2009 / Details: Double Flat Crystal, Si (111)

Radiation

Monochromator: Double Flat Crystal, Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.11587 Å / Relative weight: 1

Reflection

Resolution: 2.8→47.664 Å / Num. all: 47736 / Num. obs: 47736 / % possible obs: 99.8 % / Redundancy: 3.6 % / R_merge(I) obs: 0.109 / Net I/σ(I): 9.2

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	R_sym value	Diffraction-ID	% possible all
2.8-2.95	3.7	0.659	1.2	0.659	1	99.9
2.95-3.13	3.7	0.405	1.9	0.405	1	99.8
3.13-3.35	3.6	0.248	3.1	0.248	1	99.8
3.35-3.61	3.6	0.166	4.6	0.166	1	100
3.61-3.96	3.6	0.112	6.6	0.112	1	99.8
3.96-4.43	3.6	0.08	8.8	0.08	1	99.9
4.43-5.11	3.5	0.068	9.7	0.068	1	99.8
5.11-6.26	3.4	0.066	10.4	0.066	1	99.1
6.26-8.85	3.6	0.046	13.3	0.046	1	99.3
8.85-47.664	3.7	0.039	13.9	0.039	1	99.4

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Processing

Software

Name	Version	Classification
SCALA	3.3.9	data processing
PHENIX	1.6.4_486	refinement
PDB_EXTRACT	3.1	data extraction
ADSC	Quantum	data collection
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3PPC

3ppc

Resolution: 2.8→47.664 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.48 / σ(F): 1.35 / Phase error: 28.88 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2756	2028	4.25 %
R_work	0.2103	-	-
obs	0.2132	47729	99.72 %
all	-	47736	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 35.532 Å² / k_sol: 0.285 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.0267 Å²	0 Å²	6.934 Å²
2-	-	-5.0978 Å²	0 Å²
3-	-	-	0.0711 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→47.664 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10989	0	0	51	11040

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11223
X-RAY DIFFRACTION	f_angle_d	1.153	15343
X-RAY DIFFRACTION	f_dihedral_angle_d	14.095	3846
X-RAY DIFFRACTION	f_chiral_restr	0.072	1800
X-RAY DIFFRACTION	f_plane_restr	0.005	2010

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	5290	X-RAY DIFFRACTION	POSITIONAL
1	2	B	5290	X-RAY DIFFRACTION	POSITIONAL	0.056

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 (%)
2.8-2.8701	0.4438	144	0.3637	3222	X-RAY DIFFRACTION	100
2.8701-2.9476	0.3774	131	0.3066	3233	X-RAY DIFFRACTION	100
2.9476-3.0344	0.3535	165	0.2789	3221	X-RAY DIFFRACTION	100
3.0344-3.1323	0.3364	137	0.2477	3264	X-RAY DIFFRACTION	100
3.1323-3.2442	0.3293	144	0.2415	3257	X-RAY DIFFRACTION	100
3.2442-3.3741	0.3383	144	0.2409	3273	X-RAY DIFFRACTION	100
3.3741-3.5276	0.3077	142	0.2448	3271	X-RAY DIFFRACTION	100
3.5276-3.7135	0.3033	138	0.2179	3247	X-RAY DIFFRACTION	100
3.7135-3.9461	0.2697	148	0.196	3275	X-RAY DIFFRACTION	100
3.9461-4.2506	0.2627	146	0.1757	3252	X-RAY DIFFRACTION	100
4.2506-4.678	0.2064	149	0.1543	3283	X-RAY DIFFRACTION	100
4.678-5.3541	0.2104	159	0.1664	3266	X-RAY DIFFRACTION	100
5.3541-6.7426	0.2751	134	0.2116	3268	X-RAY DIFFRACTION	98
6.7426-47.6706	0.2319	147	0.1935	3369	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	0.078	0.0795	0.0708	0.7954	0.1969	0.3772	-0.107	0.0626	0.1496	-0.0919	0.231	0.5801	-0.2472	0.0187	-0.1313	0.3154	-0.1097	0.1102	0.1193	0.0431	0.2643	-22.0797	-8.5558	51.1089
2	0.7502	0.1611	0.5449	1.1459	0.0117	0.6344	-0.1197	0.074	0.0409	0.025	0.0912	0.2692	-0.3159	0.1766	0.0717	0.2537	-0.0835	-0.0899	0.109	-0.0284	0.2375	-18.6702	-5.8854	35.8124
3	1.0757	0.4172	-0.4345	1.3455	-0.1188	0.3833	0.1335	-0.3212	0.4007	0.3877	0.119	0.3378	-0.2265	0.0661	-0.1921	0.2782	-0.0694	0.0841	0.1051	-0.0067	0.1009	-10.5212	5.5564	56.5417
4	1.2686	0.1896	-1.1081	0.0946	-0.3102	1.2461	-0.5885	-0.0937	-0.6636	-0.063	0.0483	-0.1053	0.6478	0.1309	0.5303	0.535	0.0172	0.3542	0.0713	0.067	0.3327	12.8154	-25.9872	39.6906
5	1.3959	0.8924	-1.2485	0.6493	-0.8978	1.4354	-0.3017	-0.1098	-0.4946	-0.0482	-0.1598	-0.2766	0.3787	0.0648	0.358	0.2366	-0.0661	0.1452	0.0593	-0.028	0.1555	10.9104	-16.7687	45.5228
6	0.0698	0.0641	-0.0751	0.4668	-0.0331	0.2654	-0.1074	0.0287	-0.025	0.1018	-0.0739	-0.0548	0.2146	-0.1762	0.1023	0.3226	-0.1463	0.1249	0.1364	-0.1166	0.1333	8.4299	-16.105	22.1153
7	0.3788	-0.1672	0.3595	0.5173	-0.1855	0.3662	-0.0724	-0.0998	0.0238	-0.1694	0.0594	0.2096	-0.0387	-0.1028	-0.0058	0.0742	0.035	-0.0566	0.0748	-0.0183	0.2091	-54.9518	-35.8607	-5.7511
8	0.0342	0.0586	-0.0991	0.4211	-0.3529	0.4391	-0.1459	-0.0753	-0.0204	-0.3438	-0.0107	-0.0916	0.384	0.1271	-0.1791	-0.0364	0.0629	-0.1106	0.0608	-0.0097	0.0516	-46.7944	-49.6185	2.0187
9	0.9283	0.2963	-0.9912	0.2173	-0.1257	1.4978	0.4621	-0.0768	0.4648	0.3899	-0.0212	0.2349	-0.6124	0.173	-0.4179	0.6288	-0.1033	0.3731	0.1098	-0.0367	0.2766	-58.2303	-18.0626	28.8471
10	0.785	0.6753	-0.4918	1.249	-0.9875	0.8276	0.3112	-0.0968	0.2086	0.4448	-0.1438	0.3662	-0.3573	0.2022	-0.1205	0.1787	-0.0999	0.0819	0.0888	-0.0097	0.1407	-52.1802	-28.0497	26.0662
11	0.2945	-0.0458	-0.0855	0.1065	0.0514	0.1283	-0.2967	0.031	-0.3316	0.3571	0.0672	0.1619	0.1674	0.0072	0.2048	0.3772	0.0369	0.2372	0.1129	-0.0641	0.2754	-74.2282	-31.6212	28.1205
12	0.2933	-0.1708	-0.1293	0.2872	-0.2347	0.5771	0.1417	0.0607	0.0359	-0.0133	0.0388	0.2559	-0.1567	-0.0824	-0.1843	0.4024	0.1987	0.4796	0.239	0.2326	0.5769	-77.898	-17.3717	23.0402

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:101)
2	X-RAY DIFFRACTION	2	(chain A and resid 102:144)
3	X-RAY DIFFRACTION	3	(chain A and resid 145:395)
4	X-RAY DIFFRACTION	4	(chain A and resid 396:505)
5	X-RAY DIFFRACTION	5	(chain A and resid 506:660)
6	X-RAY DIFFRACTION	6	(chain A and resid 663:766)
7	X-RAY DIFFRACTION	7	(chain B and resid 1:137)
8	X-RAY DIFFRACTION	8	(chain B and resid 138:399)
9	X-RAY DIFFRACTION	9	(chain B and resid 400:507)
10	X-RAY DIFFRACTION	10	(chain B and resid 508:655)
11	X-RAY DIFFRACTION	11	(chain B and resid 656:735)
12	X-RAY DIFFRACTION	12	(chain B and resid 736:767)

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