PDB-5z5c: Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) f...

ID or keywords:

Entry

Database: PDB / ID: 5z5c

Title

Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) from Fusobacterium nucleatum: lysine-dimethylated form

Components

Cysteine synthase

Keywords

TRANSFERASE / Pyridoxal 5'-phosphate dependent enzyme / Internal aldimine

Function / homology

Function and homology information

L-cysteine desulfhydrase activity / cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine / cytoplasm
Similarity search - Function

Biological species

Fusobacterium nucleatum subsp. nucleatum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.07 Å

Authors

Kezuka, Y. / Yoshida, Y. / Nonaka, T.

Funding support

Japan, 2items

Citation

Journal: Biochem. J. / Year: 2018
Title: Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen sulfide-producing oral pathogen,
Authors: Kezuka, Y. / Ishida, T. / Yoshida, Y. / Nonaka, T.

History

Deposition	Jan 17, 2018	Deposition site: PDBJ / Processing site: PDBJ
Supersession	Feb 14, 2018	ID: 5B54
Revision 1.0	Feb 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 7, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Apr 9, 2025	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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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Validation report

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Related structure data

Related structure data	5b55C C: citing same article (ref.)
Similar structure data	5b53-1 2nap-d 2jim-d 4yzz-d 2ecq-1 4wtj-d 2jir-d 3qgd-1 5pzo-2 3gsz-1 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
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (3)

Deposited unit

A: Cysteine synthase

B: Cysteine synthase

C: Cysteine synthase

D: Cysteine synthase

hetero molecules

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

1

A: Cysteine synthase

B: Cysteine synthase

hetero molecules

defined by author&software
Evidence: gel filtration
77.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Cysteine synthase

D: Cysteine synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	57.760, 136.160, 171.680
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	C
3	1	D
1	2	A
2	2	C
3	2	D

NCS domain segments:

Refine code: 5

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	ILE	ILE	TYR	TYR	A	A	45 - 143	49 - 147
2	1	1	ILE	ILE	TYR	TYR	C	C	45 - 143	49 - 147
3	1	1	ILE	ILE	TYR	TYR	D	D	45 - 143	49 - 147
1	1	2	SER	SER	MLY	MLY	A	A	154 - 330	158 - 334
2	1	2	SER	SER	MLY	MLY	C	C	154 - 330	158 - 334
3	1	2	SER	SER	MLY	MLY	D	D	154 - 330	158 - 334
1	2	2	MET	MET	MLY	MLY	A	A	6 - 35	10 - 39
2	2	2	MET	MET	MLY	MLY	C	C	6 - 35	10 - 39
3	2	2	MET	MET	MLY	MLY	D	D	6 - 35	10 - 39

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.999087, -0.033312, 0.026763), (0.039503, -0.481215, 0.875712), (-0.016292, 0.875969, 0.482092)	32.99995, -16.1566, -26.61307
3	given	(0.644322, -0.709014, 0.286615), (-0.591519, -0.699589, -0.400849), (0.48472, 0.088738, -0.870156)	-28.03963, 70.91207, 31.62321

#1: Protein	Cysteine synthase Mass: 38565.102 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131) (bacteria) Strain: ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131 / Gene: FN1055 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8REP3, cysteine synthase
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H₂O
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: 2.3 Å³/Da / Density % sol: 46 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 24% (W/V) PEG 3350, 0.1M HEPES PH 7.5, 0.2M MAGNESIUM CHLORIDE HEXAHYDRATE

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Data collection

Diffraction	Mean temperature: 95 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 20, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.07→42.66 Å / Num. obs: 83053 / % possible obs: 99.6 % / Redundancy: 7 % / R_merge(I) obs: 0.051 / Net I/σ(I): 22.3
Reflection shell	Resolution: 2.07→2.12 Å / Redundancy: 6.2 % / R_merge(I) obs: 0.245 / Mean I/σ(I) obs: 7.2 / % possible all: 98.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0189	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Resolution: 2.07→40.93 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.924 / SU B: 11.548 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.189 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24177	4180	5 %	RANDOM
R_work	0.18561	-	-	-
obs	0.18839	78808	99.47 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 38.583 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.91 Å²	0 Å²	0 Å²
2-	-	1.63 Å²	0 Å²
3-	-	-	-2.54 Å²

Refinement step

Cycle: 1 / Resolution: 2.07→40.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10401	0	63	373	10837

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.017	10633
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.019	10026
X-RAY DIFFRACTION	r_angle_refined_deg	1.597	1.736	14292
X-RAY DIFFRACTION	r_angle_other_deg	1.002	2.718	23443
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.804	5	1329
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.656	25.261	422
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.832	15	1478
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.91	15	40
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	1620
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	11516
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.019	1972
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
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	0.983	1.799	5322
X-RAY DIFFRACTION	r_mcbond_other	0.983	1.799	5321
X-RAY DIFFRACTION	r_mcangle_it	1.633	2.691	6646
X-RAY DIFFRACTION	r_mcangle_other	1.633	2.691	6647
X-RAY DIFFRACTION	r_scbond_it	1.154	2.005	5311
X-RAY DIFFRACTION	r_scbond_other	1.154	2.005	5312
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.915	2.928	7646
X-RAY DIFFRACTION	r_long_range_B_refined	3.109	21.905	11375
X-RAY DIFFRACTION	r_long_range_B_other	3.107	21.905	11367
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	581	MEDIUM POSITIONAL	0.13	0.5
1	2	C	581	MEDIUM POSITIONAL	0.19	0.5
1	3	D	581	MEDIUM POSITIONAL	0.17	0.5
1	1	A	931	LOOSE POSITIONAL	0.63	5
1	2	C	931	LOOSE POSITIONAL	0.6	5
1	3	D	931	LOOSE POSITIONAL	0.78	5
1	1	A	581	MEDIUM THERMAL	4.12	2
1	2	C	581	MEDIUM THERMAL	4.22	2
1	3	D	581	MEDIUM THERMAL	2.01	2
1	1	A	931	LOOSE THERMAL	4.21	10
1	2	C	931	LOOSE THERMAL	4.67	10
1	3	D	931	LOOSE THERMAL	2.41	10
2	1	A	1216	MEDIUM POSITIONAL	0.17	0.5
2	2	C	1216	MEDIUM POSITIONAL	0.17	0.5
2	3	D	1216	MEDIUM POSITIONAL	0.22	0.5
2	1	A	1934	LOOSE POSITIONAL	0.61	5
2	2	C	1934	LOOSE POSITIONAL	0.51	5
2	3	D	1934	LOOSE POSITIONAL	0.58	5
2	1	A	1216	MEDIUM THERMAL	2.4	2
2	2	C	1216	MEDIUM THERMAL	3.64	2
2	3	D	1216	MEDIUM THERMAL	4.65	2
2	1	A	1934	LOOSE THERMAL	2.76	10
2	2	C	1934	LOOSE THERMAL	3.99	10
2	3	D	1934	LOOSE THERMAL	4.68	10

LS refinement shell

Resolution: 2.07→2.124 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.289	309	-
R_work	0.23	5631	-
obs	-	-	97.89 %

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	0.4106	-0.1561	-0.1251	0.2217	0.2159	0.7464	-0.0132	0.0664	-0.138	-0.0085	-0.1322	-0.0284	-0.1538	-0.1289	0.1454	0.069	0.0432	-0.0495	0.209	-0.0533	0.239	4.5323	18.1294	-9.1081
2	0.2426	-0.1605	-0.0301	0.3728	0.459	0.8715	-0.0345	-0.1404	-0.0855	-0.1655	-0.053	0.0274	-0.4477	-0.2133	0.0876	0.2887	0.1323	-0.1271	0.238	-0.0114	0.214	1.3845	37.9874	12.8996
3	1.0357	0.4907	0.9478	0.3822	0.6322	1.1019	0.058	0.3004	0.0485	0.1273	-0.0335	0.0176	0.1776	0.0862	-0.0244	0.0813	-0.0346	-0.0009	0.3197	-0.0239	0.1897	29.6981	0.1473	37.6443
4	0.2464	0.2588	0.4377	0.4842	0.6117	0.9068	0.1271	-0.0917	0.1638	0.24	-0.2711	0.0349	0.313	-0.2253	0.144	0.157	-0.1203	0.0376	0.2849	-0.0432	0.2514	32.808	10.5461	65.6025

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 335
2	X-RAY DIFFRACTION	1	A	401 - 402
3	X-RAY DIFFRACTION	1	A	501 - 622
4	X-RAY DIFFRACTION	2	B	0 - 335
5	X-RAY DIFFRACTION	2	B	401
6	X-RAY DIFFRACTION	2	B	501 - 568
7	X-RAY DIFFRACTION	3	C	4 - 335
8	X-RAY DIFFRACTION	3	C	401 - 402
9	X-RAY DIFFRACTION	3	C	501 - 599
10	X-RAY DIFFRACTION	4	D	4 - 335
11	X-RAY DIFFRACTION	4	D	401 - 402
12	X-RAY DIFFRACTION	4	D	501 - 584

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