PDB-3gwp: Crystal structure of carbon-sulfur lyase involved in aluminum res...

ID or keywords:

Entry

Database: PDB / ID: 3gwp

Title

Crystal structure of carbon-sulfur lyase involved in aluminum resistance (YP_878183.1) from CLOSTRIDIUM NOVYI NT at 2.90 A resolution

Components

carbon-sulfur lyase involved in aluminum resistance

Keywords

LYASE / YP_878183.1 / carbon-sulfur lyase involved in aluminum resistance / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2

Function / homology

Function and homology information

Putative methionine gamma-lyase / Methionine gamma-lyase / Methioning gamme-lyase, C-terminal domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology

Biological species

Clostridium novyi NT (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

molecular replacement / Resolution: 2.9 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of carbon-sulfur lyase involved in aluminum resistance (YP_878183.1) from CLOSTRIDIUM NOVYI NT at 2.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Apr 1, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 14, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3	Jul 24, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4	Feb 1, 2023	Group: Database references / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5	Sep 20, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.6	Nov 22, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3gwp.cif.gz	321 KB	Display	PDBx/mmCIF format
PDB format	pdb3gwp.ent.gz	258.9 KB	Display	PDB format
PDBx/mmJSON format	3gwp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3gwp_validation.pdf.gz	457.3 KB	Display	wwPDB validaton report
Full document	3gwp_full_validation.pdf.gz	479.2 KB	Display
Data in XML	3gwp_validation.xml.gz	57 KB	Display
Data in CIF	3gwp_validation.cif.gz	77.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gw/3gwp ftp://data.pdbj.org/pub/pdb/validation_reports/gw/3gwp	HTTPS FTP

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Related structure data

Related structure data	3fd0S S: Starting model for refinement
Similar structure data	3ht4-1 3ht4-2 3i16-d 3hvy-d 3fd0-1 6ft9-d 2iqf-1 2a9e-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: 391679

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: carbon-sulfur lyase involved in aluminum resistance

B: carbon-sulfur lyase involved in aluminum resistance

C: carbon-sulfur lyase involved in aluminum resistance

D: carbon-sulfur lyase involved in aluminum resistance

192 kDa, 4 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)	78.740, 108.948, 207.642
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
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

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLY	GLY	HIS	HIS	4	A	A	0 - 60	1 - 61
2	1	GLY	GLY	HIS	HIS	4	B	B	0 - 60	1 - 61
3	1	GLY	GLY	HIS	HIS	4	C	C	0 - 60	1 - 61
4	1	GLY	GLY	HIS	HIS	4	D	D	0 - 60	1 - 61
1	2	PHE	PHE	SER	SER	6	A	A	61 - 65	62 - 66
2	2	PHE	PHE	SER	SER	6	B	B	61 - 65	62 - 66
3	2	PHE	PHE	SER	SER	6	C	C	61 - 65	62 - 66
4	2	PHE	PHE	SER	SER	6	D	D	61 - 65	62 - 66
1	3	GLY	GLY	PRO	PRO	4	A	A	66 - 124	67 - 125
2	3	GLY	GLY	PRO	PRO	4	B	B	66 - 124	67 - 125
3	3	GLY	GLY	PRO	PRO	4	C	C	66 - 124	67 - 125
4	3	GLY	GLY	PRO	PRO	4	D	D	66 - 124	67 - 125
1	4	TYR	TYR	LEU	LEU	6	A	A	125 - 143	126 - 144
2	4	TYR	TYR	LEU	LEU	6	B	B	125 - 143	126 - 144
3	4	TYR	TYR	LEU	LEU	6	C	C	125 - 143	126 - 144
4	4	TYR	TYR	LEU	LEU	6	D	D	125 - 143	126 - 144
1	5	LYS	LYS	SER	SER	4	A	A	144 - 184	145 - 185
2	5	LYS	LYS	SER	SER	4	B	B	144 - 184	145 - 185
3	5	LYS	LYS	SER	SER	4	C	C	144 - 184	145 - 185
4	5	LYS	LYS	SER	SER	4	D	D	144 - 184	145 - 185
1	6	THR	THR	ILE	ILE	6	A	A	185 - 195	186 - 196
2	6	THR	THR	ILE	ILE	6	B	B	185 - 195	186 - 196
3	6	THR	THR	ILE	ILE	6	C	C	185 - 195	186 - 196
4	6	THR	THR	ILE	ILE	6	D	D	185 - 195	186 - 196
1	7	GLU	GLU	PHE	PHE	4	A	A	196 - 360	197 - 361
2	7	GLU	GLU	PHE	PHE	4	B	B	196 - 360	197 - 361
3	7	GLU	GLU	PHE	PHE	4	C	C	196 - 360	197 - 361
4	7	GLU	GLU	PHE	PHE	4	D	D	196 - 360	197 - 361
1	8	VAL	VAL	GLY	GLY	6	A	A	361 - 380	362 - 381
2	8	VAL	VAL	GLY	GLY	6	B	B	361 - 380	362 - 381
3	8	VAL	VAL	GLY	GLY	6	C	C	361 - 380	362 - 381
4	8	VAL	VAL	GLY	GLY	6	D	D	361 - 380	362 - 381
1	9	ALA	ALA	ASP	ASP	4	A	A	381 - 393	382 - 394
2	9	ALA	ALA	ASP	ASP	4	B	B	381 - 393	382 - 394
3	9	ALA	ALA	ASP	ASP	4	C	C	381 - 393	382 - 394
4	9	ALA	ALA	ASP	ASP	4	D	D	381 - 393	382 - 394
1	10	ALA	ALA	TYR	TYR	6	A	A	394 - 400	395 - 401
2	10	ALA	ALA	TYR	TYR	6	B	B	394 - 400	395 - 401
3	10	ALA	ALA	TYR	TYR	6	C	C	394 - 400	395 - 401
4	10	ALA	ALA	TYR	TYR	6	D	D	394 - 400	395 - 401
1	11	ILE	ILE	ALA	ALA	4	A	A	401 - 420	402 - 421
2	11	ILE	ILE	ALA	ALA	4	B	B	401 - 420	402 - 421
3	11	ILE	ILE	ALA	ALA	4	C	C	401 - 420	402 - 421
4	11	ILE	ILE	ALA	ALA	4	D	D	401 - 420	402 - 421
1	12	LEU	LEU	ILE	ILE	6	A	A	421 - 424	422 - 425
2	12	LEU	LEU	ILE	ILE	6	B	B	421 - 424	422 - 425
3	12	LEU	LEU	ILE	ILE	6	C	C	421 - 424	422 - 425
4	12	LEU	LEU	ILE	ILE	6	D	D	421 - 424	422 - 425

#1: Protein	carbon-sulfur lyase involved in aluminum resistance / Aluminum resistance protein Mass: 48011.809 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium novyi NT (bacteria) / Gene: NT01CX_2110, YP_878183.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A0Q0N1
Sequence details	SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE

#1: Protein

carbon-sulfur lyase involved in aluminum resistance / Aluminum resistance protein

Mass: 48011.809 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Clostridium novyi NT (bacteria) / Gene: NT01CX_2110, YP_878183.1 / Plasmid: SpeedET / Production host:

Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A0Q0N1

Sequence details

SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...

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Experiment

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

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.32	46.95
2

Crystal grow

Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.2000M (NH4)2Tartrate, 20.0000% PEG-3350, No Buffer pH 6.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.97918

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 10, 2008 / Details: Flat collimating mirror, toroid focusing mirror

Radiation

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

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 2.9→29.775 Å / Num. obs: 40426 / % possible obs: 99.9 % / Redundancy: 3.7 % / B_iso Wilson estimate: 42.549 Å² / R_merge(I) obs: 0.243 / R_sym value: 0.243 / Net I/σ(I): 3.121

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.9-2.98	3.7	0.749	1	10891	2934	0.749	100
2.98-3.06	3.7	0.655	1.2	10707	2889	0.655	100
3.06-3.15	3.7	0.547	1.4	10439	2797	0.547	100
3.15-3.24	3.7	0.466	1.7	10047	2698	0.466	100
3.24-3.35	3.7	0.393	2	9757	2644	0.393	100
3.35-3.47	3.7	0.34	2.3	9501	2567	0.34	100
3.47-3.6	3.7	0.282	2.8	9061	2444	0.282	100
3.6-3.74	3.7	0.259	3	8864	2406	0.259	100
3.74-3.91	3.7	0.221	3.5	8421	2288	0.221	100
3.91-4.1	3.7	0.183	4.2	7990	2165	0.183	100
4.1-4.32	3.7	0.161	4.8	7730	2094	0.161	100
4.32-4.59	3.7	0.151	5	7290	1985	0.151	100
4.59-4.9	3.7	0.146	5.2	6855	1872	0.146	100
4.9-5.29	3.6	0.152	5.1	6334	1741	0.152	100
5.29-5.8	3.6	0.188	4.1	5882	1621	0.188	100
5.8-6.48	3.6	0.195	3.9	5340	1471	0.195	100
6.48-7.49	3.6	0.139	5.4	4651	1310	0.139	100
7.49-9.17	3.5	0.08	9.2	3938	1124	0.08	100
9.17-12.97	3.4	0.067	10.9	3048	898	0.067	99.9
12.97-29.77	3.2	0.061	10.5	1517	478	0.061	91.1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
PHENIX		refinement
PHASER		phasing
MolProbity	3beta29	model building
SCALA	3.2.5	data scaling
PDB_EXTRACT	3.006	data extraction
MOSFLM		data reduction

Refinement

Method to determine structure:

molecular replacement
Starting model: 3FD0

3fd0

Resolution: 2.9→29.775 Å / Cor.coef. F_o:F_c: 0.882 / Cor.coef. F_o:F_c free: 0.835 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 43.411 / SU ML: 0.364 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.465 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.271	2022	5 %	RANDOM
R_work	0.223	-	-	-
obs	0.225	40367	99.86 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 48.2 Å² / B_iso mean: 24.943 Å² / B_iso min: 18.31 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.65 Å²	0 Å²	0 Å²
2-	-	-0.4 Å²	0 Å²
3-	-	-	2.05 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→29.775 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12883	0	0	0	12883

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	13143
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	8642
X-RAY DIFFRACTION	r_angle_refined_deg	1.065	1.971	17810
X-RAY DIFFRACTION	r_angle_other_deg	0.879	3	21156
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.167	5	1699
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	24.6	24.851	569
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.036	15	2171
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.808	15	61
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	2013
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	14865
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2594
X-RAY DIFFRACTION	r_nbd_refined	0.161	0.3	3154
X-RAY DIFFRACTION	r_nbd_other	0.139	0.3	9251
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.5	6764
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.5	5682
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.5	443
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.004	0.5	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.079	0.3	3
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.123	0.3	23
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.17	0.5	5
X-RAY DIFFRACTION	r_mcbond_it	0.318	2	8878
X-RAY DIFFRACTION	r_mcbond_other	0.061	2	3499
X-RAY DIFFRACTION	r_mcangle_it	0.526	3	13418
X-RAY DIFFRACTION	r_scbond_it	0.26	2	5145
X-RAY DIFFRACTION	r_scangle_it	0.397	3	4387

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	4369	MEDIUM POSITIONAL	0.25	0.5
2	B	4369	MEDIUM POSITIONAL	0.24	0.5
3	C	4369	MEDIUM POSITIONAL	0.26	0.5
4	D	4369	MEDIUM POSITIONAL	0.36	0.5
1	A	670	LOOSE POSITIONAL	0.7	5
2	B	670	LOOSE POSITIONAL	0.77	5
3	C	670	LOOSE POSITIONAL	0.87	5
4	D	670	LOOSE POSITIONAL	1.43	5
1	A	4369	MEDIUM THERMAL	0.17	2
2	B	4369	MEDIUM THERMAL	0.18	2
3	C	4369	MEDIUM THERMAL	0.17	2
4	D	4369	MEDIUM THERMAL	0.18	2
1	A	670	LOOSE THERMAL	0.84	10
2	B	670	LOOSE THERMAL	1.38	10
3	C	670	LOOSE THERMAL	1.27	10
4	D	670	LOOSE THERMAL	1.78	10

LS refinement shell

Resolution: 2.9→2.975 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.372	142	-
R_work	0.313	2788	-
all	-	2930	-
obs	-	-	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	0.3533	0.3494	0.1721	1.0777	0.2766	0.3988	0.0315	0.0095	-0.0092	-0.036	0.0069	-0.1592	0.0423	0.136	-0.0385	-0.039	-0.0046	-0.0185	0.01	0.0311	-0.0813	9.9215	-5.1493	-11.8832
2	0.3692	0.2288	0.2971	0.3973	0.1646	0.7984	0.0271	-0.1362	0.049	0.0542	-0.0189	0.157	-0.0271	-0.2212	-0.0083	-0.0562	0.001	-0.01	-0.041	0.0257	-0.0323	-24.4906	-12.2536	-18.0264
3	1.4541	-0.0542	0.4766	0.3879	-0.2899	0.5095	-0.0954	-0.0778	0.3419	0.0654	-0.0068	-0.0792	-0.1745	0.0167	0.1022	-0.0003	-0.0227	0.0006	-0.0346	0.0364	0.0284	4.9723	29.1379	-34.5412
4	1.0396	0.518	-0.1072	0.4473	-0.3725	0.5494	0.0051	0.1389	-0.1048	-0.0745	0.0388	0.0067	0.0467	-0.0144	-0.044	-0.0113	0.0494	-0.02	-0.0471	0.0084	-0.0179	-21.9854	12.7817	-50.8674

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 426
2	X-RAY DIFFRACTION	2	B	0 - 426
3	X-RAY DIFFRACTION	3	C	0 - 425
4	X-RAY DIFFRACTION	4	D	0 - 426

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