PDB-1nzc: The high resolution structures of RmlC from Streptococcus suis in...

ID or keywords:

Entry

Database: PDB / ID: 1nzc

Title

The high resolution structures of RmlC from Streptococcus suis in complex with dTDP-D-xylose

Components

dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase

Keywords

ISOMERASE / Jelly roll-like structure / Beta sheet

Function / homology

Function and homology information

dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / polysaccharide biosynthetic process / cytosol
Similarity search - Function

Biological species

Streptococcus suis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Dong, C. / Major, L.L. / Allen, A. / Blankenfeldt, W. / Maskell, D. / Naismith, J.H.

Citation

Journal: Structure / Year: 2003
Title: High-Resolution Structures of RmlC from Streptococcus suis in Complex with Substrate Analogs Locate the Active Site of This Class of Enzyme
Authors: Dong, C. / Major, L.L. / Allen, A. / Blankenfeldt, W. / Maskell, D. / Naismith, J.H.

History

Deposition	Feb 17, 2003	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 24, 2003	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Aug 16, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	1nzc_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	1nzc_full_validation.pdf.gz	1.8 MB	Display
Data in XML	1nzc_validation.xml.gz	42.4 KB	Display
Data in CIF	1nzc_validation.cif.gz	60.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nz/1nzc ftp://data.pdbj.org/pub/pdb/validation_reports/nz/1nzc	HTTPS FTP

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Related structure data

Related structure data	1nxmC 1nywSC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2ixl-1 4rv5-2 4tmx-1 6rkf-5 1xsr-d 6rkf-2 1xsq-d 4oat-1 2ixk-d 4tn1-1 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

Deposited unit

A: dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase

B: dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase

C: dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase

D: dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase

hetero molecules

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

1

A: dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase

B: dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase

hetero molecules

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

2

C: dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase

D: dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.850, 140.866, 53.699
Angle α, β, γ (deg.)	90.00, 92.72, 90.00
Int Tables number	4
Cell setting	monoclinic
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
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	LEU	LEU	PRO	PRO	2	A	A	22 - 27	22 - 27
2	1	LEU	LEU	PRO	PRO	2	B	B	22 - 27	22 - 27
3	1	LEU	LEU	PRO	PRO	2	C	C	22 - 27	22 - 27
4	1	LEU	LEU	PRO	PRO	2	D	D	22 - 27	22 - 27
5	2	LEU	LEU	SER	SER	2	A	A	60 - 67	60 - 67
6	2	LEU	LEU	SER	SER	2	B	B	60 - 67	60 - 67
7	2	LEU	LEU	SER	SER	2	C	C	60 - 67	60 - 67
8	2	LEU	LEU	SER	SER	2	D	D	60 - 67	60 - 67
9	3	VAL	VAL	ALA	ALA	4	A	A	71 - 77	71 - 77
10	3	VAL	VAL	ALA	ALA	4	B	B	71 - 77	71 - 77
11	3	VAL	VAL	ALA	ALA	4	C	C	71 - 77	71 - 77
12	3	VAL	VAL	ALA	ALA	4	D	D	71 - 77	71 - 77
13	4	TRP	TRP	VAL	VAL	2	A	A	80 - 86	80 - 86
14	4	TRP	TRP	VAL	VAL	2	B	B	80 - 86	80 - 86
15	4	TRP	TRP	VAL	VAL	2	C	C	80 - 86	80 - 86
16	4	TRP	TRP	VAL	VAL	2	D	D	80 - 86	80 - 86
17	5	GLY	GLY	GLU	GLU	2	A	A	90 - 101	90 - 101
18	5	GLY	GLY	GLU	GLU	2	B	B	90 - 101	90 - 101
19	5	GLY	GLY	GLU	GLU	2	C	C	90 - 101	90 - 101
20	5	GLY	GLY	GLU	GLU	2	D	D	90 - 101	90 - 101
21	6	GLY	GLY	ILE	ILE	2	A	A	106 - 113	106 - 113
22	6	GLY	GLY	ILE	ILE	2	B	B	106 - 113	106 - 113
23	6	GLY	GLY	ILE	ILE	2	C	C	106 - 113	106 - 113
24	6	GLY	GLY	ILE	ILE	2	D	D	106 - 113	106 - 113
25	7	SER	SER	PRO	PRO	2	A	A	116 - 122	116 - 122
26	7	SER	SER	PRO	PRO	2	B	B	116 - 122	116 - 122
27	7	SER	SER	PRO	PRO	2	C	C	116 - 122	116 - 122
28	7	SER	SER	PRO	PRO	2	D	D	116 - 122	116 - 122
29	8	VAL	VAL	VAL	VAL	2	A	A	125 - 131	125 - 131
30	8	VAL	VAL	VAL	VAL	2	B	B	125 - 131	125 - 131
31	8	VAL	VAL	VAL	VAL	2	C	C	125 - 131	125 - 131
32	8	VAL	VAL	VAL	VAL	2	D	D	125 - 131	125 - 131
33	9	VAL	VAL	VAL	VAL	2	A	A	136 - 142	136 - 142
34	9	VAL	VAL	VAL	VAL	2	B	B	136 - 142	136 - 142
35	9	VAL	VAL	VAL	VAL	2	C	C	136 - 142	136 - 142
36	9	VAL	VAL	VAL	VAL	2	D	D	136 - 142	136 - 142
37	10	PHE	PHE	MET	MET	4	A	A	6 - 21	6 - 21
38	10	PHE	PHE	MET	MET	4	B	B	6 - 21	6 - 21
39	10	PHE	PHE	MET	MET	4	C	C	6 - 21	6 - 21
40	10	PHE	PHE	MET	MET	4	D	D	6 - 21	6 - 21
41	11	PRO	PRO	LYS	LYS	4	A	A	27 - 59	27 - 59
42	11	PRO	PRO	LYS	LYS	4	B	B	27 - 59	27 - 59
43	11	PRO	PRO	LYS	LYS	4	C	C	27 - 59	27 - 59
44	11	PRO	PRO	LYS	LYS	4	D	D	27 - 59	27 - 59
45	12	ARG	ARG	ASN	ASN	6	A	A	68 - 70	68 - 70
46	12	ARG	ARG	ASN	ASN	6	B	B	68 - 70	68 - 70
47	12	ARG	ARG	ASN	ASN	6	C	C	68 - 70	68 - 70
48	12	ARG	ARG	ASN	ASN	6	D	D	68 - 70	68 - 70
49	13	GLU	GLU	PRO	PRO	6	A	A	78 - 79	78 - 79
50	13	GLU	GLU	PRO	PRO	6	B	B	78 - 79	78 - 79
51	13	GLU	GLU	PRO	PRO	6	C	C	78 - 79	78 - 79
52	13	GLU	GLU	PRO	PRO	6	D	D	78 - 79	78 - 79
53	14	ALA	ALA	GLY	GLY	6	A	A	87 - 89	87 - 89
54	14	ALA	ALA	GLY	GLY	6	B	B	87 - 89	87 - 89
55	14	ALA	ALA	GLY	GLY	6	C	C	87 - 89	87 - 89
56	14	ALA	ALA	GLY	GLY	6	D	D	87 - 89	87 - 89
57	15	GLY	GLY	PHE	PHE	6	A	A	102 - 105	102 - 105
58	15	GLY	GLY	PHE	PHE	6	B	B	102 - 105	102 - 105
59	15	GLY	GLY	PHE	PHE	6	C	C	102 - 105	102 - 105
60	15	GLY	GLY	PHE	PHE	6	D	D	102 - 105	102 - 105
61	16	ASP	ASP	ALA	ALA	6	A	A	114 - 115	114 - 115
62	16	ASP	ASP	ALA	ALA	6	B	B	114 - 115	114 - 115
63	16	ASP	ASP	ALA	ALA	6	C	C	114 - 115	114 - 115
64	16	ASP	ASP	ALA	ALA	6	D	D	114 - 115	114 - 115
65	17	ARG	ARG	GLY	GLY	6	A	A	123 - 124	123 - 124
66	17	ARG	ARG	GLY	GLY	6	B	B	123 - 124	123 - 124
67	17	ARG	ARG	GLY	GLY	6	C	C	123 - 124	123 - 124
68	17	ARG	ARG	GLY	GLY	6	D	D	123 - 124	123 - 124
69	18	LEU	LEU	PHE	PHE	6	A	A	132 - 135	132 - 135
70	18	LEU	LEU	PHE	PHE	6	B	B	132 - 135	132 - 135
71	18	LEU	LEU	PHE	PHE	6	C	C	132 - 135	132 - 135
72	18	LEU	LEU	PHE	PHE	6	D	D	132 - 135	132 - 135
73	19	ASN	ASN	LEU	LEU	5	A	A	143 - 197	143 - 197
74	19	ASN	ASN	LEU	LEU	5	B	B	143 - 197	143 - 197
75	19	ASN	ASN	LEU	LEU	5	C	C	143 - 197	143 - 197
76	19	ASN	ASN	LEU	LEU	5	D	D	143 - 197	143 - 197

#1: Protein	dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase / E.C.5.1.3.13 / dTDP-4-dehydrorhamnose 3 / 5-epimerase Mass: 22488.295 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus suis (bacteria) / Strain: serotype 2 / Gene: rmlc / Plasmid: pET21(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q8GIQ0, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical	ChemComp-TDX / THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE Mass: 534.303 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₄N₂O₁₅P₂
#3: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 874 / 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: 1.88 Å³/Da / Density % sol: 33.9 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.1 M Tris, 4 mM NiCl2,10 mM dTDP-D-xylose, 35% PEG 2000, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal grow

*PLUS

Method: vapor diffusion, sitting drop

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details	Chemical formula
1	7 mg/ml	protein	1	drop
2	0.1 M	Tris-HCl	1	reservoir	pH8.2
3	4 mM		1	reservoir		NiCl2
4	35 %	PEG2000	1	reservoir
5	10 mM	dTDP-D-xylose	1	drop

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Data collection

Diffraction	Mean temperature: 120 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 28, 2001
Radiation	Monochromator: Liquid gallium cooled, bent, triangulary Si111 Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.488 Å / Relative weight: 1
Reflection	Resolution: 1.8→50.79 Å / Num. all: 63995 / Num. obs: 63969 / % possible obs: 91.8 % / Observed criterion σ(F): 2.96 / Observed criterion σ(I): 3.1 / Redundancy: 5.3 % / B_iso Wilson estimate: 21.38 Å² / R_merge(I) obs: 0.126 / R_sym value: 0.117 / Net I/σ(I): 3.8
Reflection shell	Resolution: 1.8→1.81 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.112 / Mean I/σ(I) obs: 8.1 / Num. unique all: 500 / R_sym value: 0.085 / % possible all: 43.3
Reflection	PLUS Num. obs: 63995 / Num. measured all: 659635 / R_merge(I) obs*: 0.117
Reflection shell	PLUS % possible obs: 43.3 % / R_merge(I) obs*: 0.085

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing
REFMAC	5.1.19	refinement
CCP4	(SCALA)	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1NYW

1nyw

Resolution: 1.8→70.71 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.941 / SU B: 3.022 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 2.574 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21562	3217	5 %	RANDOM
R_work	0.16445	-	-	-
obs	0.16698	60716	91.8 %	-
all	-	87974	-	-

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: 17.913 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.44 Å²	0 Å²	-0.03 Å²
2-	-	-0.02 Å²	0 Å²
3-	-	-	0.46 Å²

Refine analyze

Luzzati coordinate error free: 0.142 Å

Refinement step

Cycle: LAST / Resolution: 1.8→70.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6304	0	138	874	7316

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.021	6627
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	5736
X-RAY DIFFRACTION	r_angle_refined_deg	1.577	1.969	9010
X-RAY DIFFRACTION	r_angle_other_deg	0.911	3	13417
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.41	5	776
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	941
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	7316
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1388
X-RAY DIFFRACTION	r_nbd_refined	0.196	0.2	1187
X-RAY DIFFRACTION	r_nbd_other	0.256	0.2	6640
X-RAY DIFFRACTION	r_nbtor_other	0.089	0.2	3658
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.176	0.2	622
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.289	0.2	31
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.271	0.2	117
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.35	0.2	81
X-RAY DIFFRACTION	r_mcbond_it	0.747	1.5	3884
X-RAY DIFFRACTION	r_mcangle_it	1.294	2	6246
X-RAY DIFFRACTION	r_scbond_it	1.847	3	2743
X-RAY DIFFRACTION	r_scangle_it	2.882	4.5	2764
X-RAY DIFFRACTION	r_rigid_bond_restr	1.119	2	6627
X-RAY DIFFRACTION	r_sphericity_free	2.886	2	927
X-RAY DIFFRACTION	r_sphericity_bonded	1.069	2	6439

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	954	tight positional	0.05	0.05
2	B	954	tight positional	0.1	0.05
3	C	954	tight positional	0.05	0.05
4	D	954	tight positional	0.04	0.05
1	A	1725	medium positional	0.71	0.5
2	B	1725	medium positional	1.2	0.5
3	C	1725	medium positional	0.69	0.5
4	D	1725	medium positional	0.66	0.5
1	A	282	loose positional	0.98	5
2	B	282	loose positional	0.9	5
3	C	282	loose positional	0.74	5
4	D	282	loose positional	0.59	5
1	A	954	tight thermal	0.11	0.5
2	B	954	tight thermal	0.11	0.5
3	C	954	tight thermal	0.09	0.5
4	D	954	tight thermal	0.1	0.5
1	A	1725	medium thermal	0.76	2
2	B	1725	medium thermal	0.83	2
3	C	1725	medium thermal	0.54	2
4	D	1725	medium thermal	0.69	2
1	A	282	loose thermal	2.06	10
2	B	282	loose thermal	2.61	10
3	C	282	loose thermal	0.88	10
4	D	282	loose thermal	2.97	10

LS refinement shell

Resolution: 1.8→1.847 Å / R_factor R_free error: 0.142 / Total num. of bins used: 20

	R_factor	Num. reflection
R_free	0.26	121
R_work	0.148	2436
obs	-	2436

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	1.0002	0.0174	0.3548	1.3336	-0.1216	1.0936	-0.026	-0.1404	0.0206	0.2321	-0.0144	-0.1809	-0.013	0.1711	0.0403	0.0361	0.0125	-0.027	0.0876	0.0125	0.0745	15.673	-0.987	19.085
2	0.8535	0.1145	0.3239	0.9506	-0.1014	0.9211	-0.0289	0.0359	0.0402	-0.1343	0.0305	0.2212	-0.0153	-0.1725	-0.0016	0.0161	0.0146	-0.0152	0.0666	0.0149	0.098	-5.832	-0.031	1.687
3	1.0268	0.2839	0.3187	0.6164	0.0612	0.8971	0.0463	-0.0758	-0.0278	0.067	-0.0209	-0.154	0.0504	0.0519	-0.0254	0.035	-0.007	0.0049	0.0081	-0.0205	0.0573	23.214	103.948	58.751
4	0.9266	0.3369	0.3728	0.9101	0.2309	0.815	-0.0776	0.1524	0.0791	-0.1907	0.0553	0.0863	-0.0489	-0.0627	0.0223	0.0514	-0.0334	0.0132	0.058	0.0017	0.025	8.46	106.138	35.697

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 197	2 - 197
2	X-RAY DIFFRACTION	2	B	B	2 - 197	2 - 197
3	X-RAY DIFFRACTION	3	C	C	4 - 197	4 - 197
4	X-RAY DIFFRACTION	4	D	D	4 - 197	4 - 197

Refinement

*PLUS

R_factor R_free: 0.216 / R_factor R_work: 0.164

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.014
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	1.58

LS refinement shell

*PLUS

Highest resolution: 1.8 Å / R_factor R_free: 0.26

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