PDB-3fem: Structure of the synthase subunit Pdx1.1 (Snz1) of PLP synthase f...

ID or keywords:

Entry

Database: PDB / ID: 3fem

Title

Structure of the synthase subunit Pdx1.1 (Snz1) of PLP synthase from Saccharomyces cerevisiae

Components

Pyridoxine biosynthesis protein SNZ1

Keywords

BIOSYNTHETIC PROTEIN / TRANSFERASE / (BETA/ALPHA)8-BARREL / SYNTHASE / Pyridoxine biosynthesis

Function / homology

Function and homology information

vitamin B6 biosynthetic process / amine-lyase activity / glutaminase complex / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / L-glutamine catabolic process / amino acid metabolic process
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.02 Å

Authors

Strohmeier, M. / Windeisen, V. / Sinning, I. / Tews, I.

Citation

Journal: Febs Lett. / Year: 2009
Title: X-ray crystal structure of Saccharomyces cerevisiae Pdx1 provides insights into the oligomeric nature of PLP synthases.
Authors: Neuwirth, M. / Strohmeier, M. / Windeisen, V. / Wallner, S. / Deller, S. / Rippe, K. / Sinning, I. / Macheroux, P. / Tews, I.

History

Deposition	Nov 30, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jun 16, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 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_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3fem.cif.gz	309.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3fem.ent.gz	255.2 KB	Display	PDB format
PDBx/mmJSON format	3fem.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fe/3fem ftp://data.pdbj.org/pub/pdb/validation_reports/fe/3fem	HTTPS FTP

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Related structure data

Related structure data	2nv1S 1znn 2iss 2nv2 S: Starting model for refinement
Similar structure data	2nv1-d 3o06-1 4fir-d 4fiq-d 3o07-1 5ig5-1 3o05-1 4h5l-d 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	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Pyridoxine biosynthesis protein SNZ1

B: Pyridoxine biosynthesis protein SNZ1

C: Pyridoxine biosynthesis protein SNZ1

D: Pyridoxine biosynthesis protein SNZ1

E: Pyridoxine biosynthesis protein SNZ1

F: Pyridoxine biosynthesis protein SNZ1

191 kDa, 6 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)	154.073, 154.218, 154.868
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
1	2	A
2	2	C
3	2	E
1	3	B
2	3	D
3	3	F

NCS domain segments:

Refine code: 1

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LYS	LYS	PRO	PRO	A	A	17 - 27	17 - 27
2	1	1	LYS	LYS	PRO	PRO	B	B	17 - 27	17 - 27
3	1	1	LYS	LYS	PRO	PRO	C	C	17 - 27	17 - 27
4	1	1	LYS	LYS	PRO	PRO	D	D	17 - 27	17 - 27
5	1	1	LYS	LYS	PRO	PRO	E	E	17 - 27	17 - 27
6	1	1	LYS	LYS	PRO	PRO	F	F	17 - 27	17 - 27
1	2	1	SER	SER	ILE	ILE	A	A	36 - 283	36 - 283
2	2	1	SER	SER	ILE	ILE	B	B	36 - 283	36 - 283
3	2	1	SER	SER	ILE	ILE	C	C	36 - 283	36 - 283
4	2	1	SER	SER	ILE	ILE	D	D	36 - 283	36 - 283
5	2	1	SER	SER	ILE	ILE	E	E	36 - 283	36 - 283
6	2	1	SER	SER	ILE	ILE	F	F	36 - 283	36 - 283
1	1	2	GLY	GLY	LEU	LEU	A	A	3 - 16	3 - 16
2	1	2	GLY	GLY	LEU	LEU	C	C	3 - 16	3 - 16
3	1	2	GLY	GLY	LEU	LEU	E	E	3 - 16	3 - 16
1	2	2	GLU	GLU	LYS	LYS	A	A	28 - 35	28 - 35
2	2	2	GLU	GLU	LYS	LYS	C	C	28 - 35	28 - 35
3	2	2	GLU	GLU	LYS	LYS	E	E	28 - 35	28 - 35
1	1	3	GLY	GLY	LEU	LEU	B	B	3 - 16	3 - 16
2	1	3	GLY	GLY	LEU	LEU	D	D	3 - 16	3 - 16
3	1	3	GLY	GLY	LEU	LEU	F	F	3 - 16	3 - 16
1	2	3	GLU	GLU	LYS	LYS	B	B	28 - 35	28 - 35
2	2	3	GLU	GLU	LYS	LYS	D	D	28 - 35	28 - 35
3	2	3	GLU	GLU	LYS	LYS	F	F	28 - 35	28 - 35

NCS ensembles :

ID
1
2
3

#1: Protein	Pyridoxine biosynthesis protein SNZ1 / PDX1 homolog 1 / p35 Mass: 31857.887 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SNZ1, Snz1p, YM6543.03, YMR096W / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03148
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Pyridoxine biosynthesis protein SNZ1 / PDX1 homolog 1 / p35

Mass: 31857.887 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Saccharomyces cerevisiae (brewer's yeast)
Gene: SNZ1, Snz1p, YM6543.03, YMR096W / Plasmid: pET21a(+) / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03148

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 6 / 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: 4.81 Å³/Da / Density % sol: 74.44 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 4M formate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-3 / Wavelength: 0.931 Å

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 16, 2007 / Details: TOROIDAL (ESRF)

Radiation

Monochromator: GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.931 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H,K,L	1	0.47
1	1	K,-L,-H	2	0.298
1	1	-L,-H,K	3	0.231

Reflection

Resolution: 3.02→20 Å / Num. all: 72026 / Num. obs: 72026 / % possible obs: 99.8 % / Observed criterion σ(I): -4 / Redundancy: 7.9 % / B_iso Wilson estimate: 79.3 Å² / R_merge(I) obs: 0.075 / Net I/σ(I): 23.4

Reflection shell

Resolution: 3.02→3.05 Å / Redundancy: 6.5 % / R_merge(I) obs: 0.416 / Mean I/σ(I) obs: 3.4 / % possible all: 96.2

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
MOLREP		phasing
REFMAC	5.5.0066	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2NV1

2nv1

Resolution: 3.02→20 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.931 / SU B: 28.838 / SU ML: 0.226 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18097	2053	2.9 %	RANDOM
R_work	0.16215	-	-	-
obs	0.16267	69465	99.66 %	-
all	-	71521	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 32.98 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-8.08 Å²	0 Å²	0 Å²
2-	-	-9.07 Å²	0 Å²
3-	-	-	17.15 Å²

Refine analyze

Luzzati coordinate error obs: 0.647 Å / Luzzati d res low obs: 8 Å

Refinement step

Cycle: LAST / Resolution: 3.02→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12594	0	0	6	12600

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	12750
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	8730
X-RAY DIFFRACTION	r_angle_refined_deg	1.284	1.985	17166
X-RAY DIFFRACTION	r_angle_other_deg	0.894	3	21582
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.408	5	1680
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.96	25.513	468
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	23.629	15	2430
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.197	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	2028
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	14022
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2208
X-RAY DIFFRACTION	r_nbd_refined	0.278	0.2	3559
X-RAY DIFFRACTION	r_nbd_other	0.225	0.2	9709
X-RAY DIFFRACTION	r_nbtor_refined	0.194	0.2	6401
X-RAY DIFFRACTION	r_nbtor_other	0.098	0.2	7588
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.186	0.2	403
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.054	0.2	15
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.294	0.2	16
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.377	0.2	25
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.372	1.5	8352
X-RAY DIFFRACTION	r_mcbond_other	0.25	1.5	3438
X-RAY DIFFRACTION	r_mcangle_it	2.644	2	13440
X-RAY DIFFRACTION	r_scbond_it	2.269	3	4398
X-RAY DIFFRACTION	r_scangle_it	3.581	4.5	3726
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	3261	tight positional	0.02	0.05
1	1	B	3261	tight positional	0.02	0.05
1	1	C	3261	tight positional	0.02	0.05
1	1	D	3261	tight positional	0.02	0.05
1	1	E	3261	tight positional	0.02	0.05
1	1	F	3261	tight positional	0.02	0.05
2	2	A	293	tight positional	0.01	0.05
2	2	B	293	tight positional	0.01	0.05
2	2	C	293	tight positional	0.01	0.05
3	3	A	293	tight positional	0.02	0.05
3	3	B	293	tight positional	0.02	0.05
3	3	C	293	tight positional	0.02	0.05
1	1	A	3261	tight thermal	0.03	0.5
1	1	B	3261	tight thermal	0.03	0.5
1	1	C	3261	tight thermal	0.03	0.5
1	1	D	3261	tight thermal	0.03	0.5
1	1	E	3261	tight thermal	0.03	0.5
1	1	F	3261	tight thermal	0.03	0.5
2	2	A	293	tight thermal	0.03	0.5
2	2	B	293	tight thermal	0.03	0.5
2	2	C	293	tight thermal	0.02	0.5
3	3	A	293	tight thermal	0.03	0.5
3	3	B	293	tight thermal	0.03	0.5
3	3	C	293	tight thermal	0.03	0.5

LS refinement shell

Resolution: 3.017→3.094 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.302	146	-
R_work	0.254	4691	-
obs	-	-	95.31 %

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	0.6153	-0.7753	0.6757	1.9199	-0.4642	1.7106	-0.0371	0.0711	0.1081	-0.0427	-0.0332	-0.1423	-0.0595	0.188	0.0702	0.2108	0.025	0.011	0.3388	0.0327	0.1356	92.2212	71.3133	40.8907
2	2.5629	-0.339	-0.1209	0.364	0.2451	1.7924	-0.0708	-0.1995	0.0953	0.1847	0.0506	-0.095	-0.0837	0.0786	0.0202	0.2635	-0.0517	-0.0885	0.1538	0.0695	0.0773	64.54	97.0813	45.3922
3	1.4986	0.6595	-0.467	0.8659	-0.7525	2.0269	0.0437	-0.1522	0.0572	0.0755	-0.0388	-0.0065	-0.2127	-0.0296	-0.0049	0.3197	0.0311	-0.0008	0.1739	-0.0389	0.109	39.8122	93.6729	74.0217
4	1.9116	0.0753	0.5033	2.6158	-0.2603	0.6047	0.0299	-0.1295	-0.0039	0.0682	-0.0886	-0.2222	-0.0749	0.1063	0.0587	0.2056	-0.0812	0.0424	0.2606	-0.0471	0.0488	42.8574	64.4366	98.0581
5	1.9705	-0.5623	-0.7967	1.4312	0.7355	0.8645	-0.0559	-0.1666	-0.112	0.0578	0.0567	-0.1717	-0.0206	0.107	-0.0008	0.3031	0.0025	-0.0163	0.2662	0.0392	0.0672	70.7005	38.8411	93.7143
6	0.8445	0.0921	-0.3817	1.8066	-0.0138	2.2238	0.0602	0.0232	0.0749	-0.002	-0.0509	-0.0768	-0.1216	0.1518	-0.0092	0.1888	0.0855	-0.0516	0.1903	-0.0708	0.0915	95.108	42.1735	64.8182

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 283
2	X-RAY DIFFRACTION	2	B	3 - 283
3	X-RAY DIFFRACTION	3	C	3 - 283
4	X-RAY DIFFRACTION	4	D	3 - 283
5	X-RAY DIFFRACTION	5	E	3 - 283
6	X-RAY DIFFRACTION	6	F	3 - 283

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