PDB-4gn3: OBody AM1L10 bound to hen egg-white lysozyme

Basic information

• Entry: Database: PDB / ID: 4gn3
• Title: OBody AM1L10 bound to hen egg-white lysozyme

Components

• Lysozyme C
• OBody AM1L10

• Keywords: HYDROLASE/DE NOVO PROTEIN / beta barrel / OB-fold / protein-protein complex / novel scaffold / muraminidase / enzyme inhibition / engineered binding protein / inhibitor / HYDROLASE-DE NOVO PROTEIN complex

Function / homology

Function:

Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm

Domain/homology:

Nucleic acid-binding proteins / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Lysozyme-like domain superfamily / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha

Component:

Lysozyme C

• Biological species: Pyrobaculum aerophilum (archaea); Gallus gallus (chicken)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
• Authors: Steemson, J.D. / Liddament, M.T.
• Citation: Journal: Plos One / Year: 2014; Title: Tracking Molecular Recognition at the Atomic Level with a New Protein Scaffold Based on the OB-Fold.; Authors: Steemson, J.D. / Baake, M. / Rakonjac, J. / Arcus, V.L. / Liddament, M.T.

History

Deposition	Aug 16, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 21, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 12, 2014	Group: Database references
Revision 1.2	Nov 27, 2024	Group: Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_site Item: _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: Lysozyme C

B: OBody AM1L10

C: Lysozyme C

D: OBody AM1L10

E: Lysozyme C

F: OBody AM1L10

G: Lysozyme C

H: OBody AM1L10

I: Lysozyme C

J: OBody AM1L10

K: Lysozyme C

L: OBody AM1L10

M: Lysozyme C

N: OBody AM1L10

O: Lysozyme C

P: OBody AM1L10

Q: Lysozyme C

R: OBody AM1L10

hetero molecules

Summary:

• 244 kDa, 18 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	243,601	45
Polymers	239,798	18
Non-polymers	3,802	27
Water	46,407	2576

1

A: Lysozyme C

B: OBody AM1L10

hetero molecules

Summary:

• defined by author
• 27.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	27,067	5
Polymers	26,644	2
Non-polymers	422	3
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

2

C: Lysozyme C

D: OBody AM1L10

hetero molecules

Summary:

• defined by author
• 27.3 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	27,251	7
Polymers	26,644	2
Non-polymers	607	5
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

3

E: Lysozyme C

F: OBody AM1L10

hetero molecules

Summary:

• defined by author
• 27.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	27,067	5
Polymers	26,644	2
Non-polymers	422	3
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

4

G: Lysozyme C

H: OBody AM1L10

hetero molecules

Summary:

• defined by author
• 27.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	27,067	5
Polymers	26,644	2
Non-polymers	422	3
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

5

I: Lysozyme C

J: OBody AM1L10

hetero molecules

Summary:

• defined by author
• 27.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	27,067	5
Polymers	26,644	2
Non-polymers	422	3
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

6

K: Lysozyme C

L: OBody AM1L10

hetero molecules

Summary:

• defined by author
• 27.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	27,067	5
Polymers	26,644	2
Non-polymers	422	3
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

7

M: Lysozyme C

N: OBody AM1L10

hetero molecules

Summary:

• defined by author
• 27.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	27,067	5
Polymers	26,644	2
Non-polymers	422	3
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

8

O: Lysozyme C

P: OBody AM1L10

hetero molecules

Summary:

• defined by author
• 27 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	26,975	4
Polymers	26,644	2
Non-polymers	330	2
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

9

Q: Lysozyme C

R: OBody AM1L10

hetero molecules

Summary:

• defined by author
• 27 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	26,975	4
Polymers	26,644	2
Non-polymers	330	2
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Unit cell

Length a, b, c (Å)	60.540, 186.250, 245.680
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	C
1	2	A
2	2	E
1	3	A
2	3	G
1	4	A
2	4	I
1	5	A
2	5	K
1	6	A
2	6	M
1	7	A
2	7	O
1	8	A
2	8	Q
1	9	B
2	9	D
1	10	B
2	10	F
1	11	B
2	11	H
1	12	B
2	12	J
1	13	B
2	13	L
1	14	B
2	14	N
1	15	B
2	15	P
1	16	B
2	16	R
1	17	C
2	17	E
1	18	C
2	18	G
1	19	C
2	19	I
1	20	C
2	20	K
1	21	C
2	21	M
1	22	C
2	22	O
1	23	C
2	23	Q
1	24	D
2	24	F
1	25	D
2	25	H
1	26	D
2	26	J
1	27	D
2	27	L
1	28	D
2	28	N
1	29	D
2	29	P
1	30	D
2	30	R
1	31	E
2	31	G
1	32	E
2	32	I
1	33	E
2	33	K
1	34	E
2	34	M
1	35	E
2	35	O
1	36	E
2	36	Q
1	37	F
2	37	H
1	38	F
2	38	J
1	39	F
2	39	L
1	40	F
2	40	N
1	41	F
2	41	P
1	42	F
2	42	R
1	43	G
2	43	I
1	44	G
2	44	K
1	45	G
2	45	M
1	46	G
2	46	O
1	47	G
2	47	Q
1	48	H
2	48	J
1	49	H
2	49	L
1	50	H
2	50	N
1	51	H
2	51	P
1	52	H
2	52	R
1	53	I
2	53	K
1	54	I
2	54	M
1	55	I
2	55	O
1	56	I
2	56	Q
1	57	J
2	57	L
1	58	J
2	58	N
1	59	J
2	59	P
1	60	J
2	60	R
1	61	K
2	61	M
1	62	K
2	62	O
1	63	K
2	63	Q
1	64	L
2	64	N
1	65	L
2	65	P
1	66	L
2	66	R
1	67	M
2	67	O
1	68	M
2	68	Q
1	69	N
2	69	P
1	70	N
2	70	R
1	71	O
2	71	Q
1	72	P
2	72	R

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-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	LYS	LYS	LEU	LEU	A	A	1 - 129	1 - 129
2	1	LYS	LYS	LEU	LEU	C	C	1 - 129	1 - 129
1	2	LYS	LYS	LEU	LEU	A	A	1 - 129	1 - 129
2	2	LYS	LYS	LEU	LEU	E	E	1 - 129	1 - 129
1	3	LYS	LYS	LEU	LEU	A	A	1 - 129	1 - 129
2	3	LYS	LYS	LEU	LEU	G	G	1 - 129	1 - 129
1	4	LYS	LYS	LEU	LEU	A	A	1 - 129	1 - 129
2	4	LYS	LYS	LEU	LEU	I	I	1 - 129	1 - 129
1	5	LYS	LYS	LEU	LEU	A	A	1 - 129	1 - 129
2	5	LYS	LYS	LEU	LEU	K	K	1 - 129	1 - 129
1	6	LYS	LYS	LEU	LEU	A	A	1 - 129	1 - 129
2	6	LYS	LYS	LEU	LEU	M	M	1 - 129	1 - 129
1	7	LYS	LYS	LEU	LEU	A	A	1 - 129	1 - 129
2	7	LYS	LYS	LEU	LEU	O	O	1 - 129	1 - 129
1	8	LYS	LYS	LEU	LEU	A	A	1 - 129	1 - 129
2	8	LYS	LYS	LEU	LEU	Q	Q	1 - 129	1 - 129
1	9	GLY	GLY	ALA	ALA	B	B	-1 - 107	3 - 112
2	9	GLY	GLY	ALA	ALA	D	D	-1 - 107	3 - 112
1	10	GLY	GLY	LYS	LYS	B	B	-1 - 106	3 - 111
2	10	GLY	GLY	LYS	LYS	F	F	-1 - 106	3 - 111
1	11	VAL	VAL	LYS	LYS	B	B	1 - 106	5 - 111
2	11	VAL	VAL	LYS	LYS	H	H	1 - 106	5 - 111
1	12	GLY	GLY	LYS	LYS	B	B	-1 - 106	3 - 111
2	12	GLY	GLY	LYS	LYS	J	J	-1 - 106	3 - 111
1	13	GLY	GLY	LYS	LYS	B	B	-1 - 106	3 - 111
2	13	GLY	GLY	LYS	LYS	L	L	-1 - 106	3 - 111
1	14	SER	SER	ASN	ASN	B	B	0 - 105	4 - 110
2	14	SER	SER	ASN	ASN	N	N	0 - 105	4 - 110
1	15	GLY	GLY	ALA	ALA	B	B	-1 - 107	3 - 112
2	15	GLY	GLY	ALA	ALA	P	P	-1 - 107	3 - 112
1	16	GLY	GLY	ALA	ALA	B	B	-1 - 107	3 - 112
2	16	GLY	GLY	ALA	ALA	R	R	-1 - 107	3 - 112
1	17	LYS	LYS	LEU	LEU	C	C	1 - 129	1 - 129
2	17	LYS	LYS	LEU	LEU	E	E	1 - 129	1 - 129
1	18	LYS	LYS	LEU	LEU	C	C	1 - 129	1 - 129
2	18	LYS	LYS	LEU	LEU	G	G	1 - 129	1 - 129
1	19	LYS	LYS	LEU	LEU	C	C	1 - 129	1 - 129
2	19	LYS	LYS	LEU	LEU	I	I	1 - 129	1 - 129
1	20	LYS	LYS	LEU	LEU	C	C	1 - 129	1 - 129
2	20	LYS	LYS	LEU	LEU	K	K	1 - 129	1 - 129
1	21	LYS	LYS	LEU	LEU	C	C	1 - 129	1 - 129
2	21	LYS	LYS	LEU	LEU	M	M	1 - 129	1 - 129
1	22	LYS	LYS	LEU	LEU	C	C	1 - 129	1 - 129
2	22	LYS	LYS	LEU	LEU	O	O	1 - 129	1 - 129
1	23	LYS	LYS	LEU	LEU	C	C	1 - 129	1 - 129
2	23	LYS	LYS	LEU	LEU	Q	Q	1 - 129	1 - 129
1	24	GLY	GLY	LYS	LYS	D	D	-1 - 106	3 - 111
2	24	GLY	GLY	LYS	LYS	F	F	-1 - 106	3 - 111
1	25	VAL	VAL	ASN	ASN	D	D	1 - 105	5 - 110
2	25	VAL	VAL	ASN	ASN	H	H	1 - 105	5 - 110
1	26	GLY	GLY	LYS	LYS	D	D	-1 - 106	3 - 111
2	26	GLY	GLY	LYS	LYS	J	J	-1 - 106	3 - 111
1	27	GLY	GLY	LYS	LYS	D	D	-1 - 106	3 - 111
2	27	GLY	GLY	LYS	LYS	L	L	-1 - 106	3 - 111
1	28	SER	SER	ASN	ASN	D	D	0 - 105	4 - 110
2	28	SER	SER	ASN	ASN	N	N	0 - 105	4 - 110
1	29	GLY	GLY	ALA	ALA	D	D	-1 - 107	3 - 112
2	29	GLY	GLY	ALA	ALA	P	P	-1 - 107	3 - 112
1	30	GLY	GLY	LYS	LYS	D	D	-1 - 106	3 - 111
2	30	GLY	GLY	LYS	LYS	R	R	-1 - 106	3 - 111
1	31	LYS	LYS	LEU	LEU	E	E	1 - 129	1 - 129
2	31	LYS	LYS	LEU	LEU	G	G	1 - 129	1 - 129
1	32	LYS	LYS	LEU	LEU	E	E	1 - 129	1 - 129
2	32	LYS	LYS	LEU	LEU	I	I	1 - 129	1 - 129
1	33	LYS	LYS	LEU	LEU	E	E	1 - 129	1 - 129
2	33	LYS	LYS	LEU	LEU	K	K	1 - 129	1 - 129
1	34	LYS	LYS	LEU	LEU	E	E	1 - 129	1 - 129
2	34	LYS	LYS	LEU	LEU	M	M	1 - 129	1 - 129
1	35	LYS	LYS	LEU	LEU	E	E	1 - 129	1 - 129
2	35	LYS	LYS	LEU	LEU	O	O	1 - 129	1 - 129
1	36	LYS	LYS	LEU	LEU	E	E	1 - 129	1 - 129
2	36	LYS	LYS	LEU	LEU	Q	Q	1 - 129	1 - 129
1	37	VAL	VAL	ASN	ASN	F	F	1 - 105	5 - 110
2	37	VAL	VAL	ASN	ASN	H	H	1 - 105	5 - 110
1	38	ALA	ALA	LYS	LYS	F	F	-3 - 108	1 - 113
2	38	ALA	ALA	LYS	LYS	J	J	-3 - 108	1 - 113
1	39	MET	MET	ALA	ALA	F	F	-2 - 107	2 - 112
2	39	MET	MET	ALA	ALA	L	L	-2 - 107	2 - 112
1	40	SER	SER	ASN	ASN	F	F	0 - 105	4 - 110
2	40	SER	SER	ASN	ASN	N	N	0 - 105	4 - 110
1	41	GLY	GLY	LYS	LYS	F	F	-1 - 106	3 - 111
2	41	GLY	GLY	LYS	LYS	P	P	-1 - 106	3 - 111
1	42	GLY	GLY	ALA	ALA	F	F	-1 - 107	3 - 112
2	42	GLY	GLY	ALA	ALA	R	R	-1 - 107	3 - 112
1	43	LYS	LYS	LEU	LEU	G	G	1 - 129	1 - 129
2	43	LYS	LYS	LEU	LEU	I	I	1 - 129	1 - 129
1	44	LYS	LYS	LEU	LEU	G	G	1 - 129	1 - 129
2	44	LYS	LYS	LEU	LEU	K	K	1 - 129	1 - 129
1	45	LYS	LYS	LEU	LEU	G	G	1 - 129	1 - 129
2	45	LYS	LYS	LEU	LEU	M	M	1 - 129	1 - 129
1	46	LYS	LYS	LEU	LEU	G	G	1 - 129	1 - 129
2	46	LYS	LYS	LEU	LEU	O	O	1 - 129	1 - 129
1	47	LYS	LYS	LEU	LEU	G	G	1 - 129	1 - 129
2	47	LYS	LYS	LEU	LEU	Q	Q	1 - 129	1 - 129
1	48	VAL	VAL	ASN	ASN	H	H	1 - 105	5 - 110
2	48	VAL	VAL	ASN	ASN	J	J	1 - 105	5 - 110
1	49	VAL	VAL	LYS	LYS	H	H	1 - 106	5 - 111
2	49	VAL	VAL	LYS	LYS	L	L	1 - 106	5 - 111
1	50	SER	SER	LYS	LYS	H	H	0 - 106	4 - 111
2	50	SER	SER	LYS	LYS	N	N	0 - 106	4 - 111
1	51	VAL	VAL	ASN	ASN	H	H	1 - 105	5 - 110
2	51	VAL	VAL	ASN	ASN	P	P	1 - 105	5 - 110
1	52	VAL	VAL	LYS	LYS	H	H	1 - 106	5 - 111
2	52	VAL	VAL	LYS	LYS	R	R	1 - 106	5 - 111
1	53	LYS	LYS	LEU	LEU	I	I	1 - 129	1 - 129
2	53	LYS	LYS	LEU	LEU	K	K	1 - 129	1 - 129
1	54	LYS	LYS	LEU	LEU	I	I	1 - 129	1 - 129
2	54	LYS	LYS	LEU	LEU	M	M	1 - 129	1 - 129
1	55	LYS	LYS	LEU	LEU	I	I	1 - 129	1 - 129
2	55	LYS	LYS	LEU	LEU	O	O	1 - 129	1 - 129
1	56	LYS	LYS	LEU	LEU	I	I	1 - 129	1 - 129
2	56	LYS	LYS	LEU	LEU	Q	Q	1 - 129	1 - 129
1	57	MET	MET	LYS	LYS	J	J	-2 - 108	2 - 113
2	57	MET	MET	LYS	LYS	L	L	-2 - 108	2 - 113
1	58	SER	SER	ASN	ASN	J	J	0 - 105	4 - 110
2	58	SER	SER	ASN	ASN	N	N	0 - 105	4 - 110
1	59	GLY	GLY	LYS	LYS	J	J	-1 - 106	3 - 111
2	59	GLY	GLY	LYS	LYS	P	P	-1 - 106	3 - 111
1	60	GLY	GLY	ALA	ALA	J	J	-1 - 107	3 - 112
2	60	GLY	GLY	ALA	ALA	R	R	-1 - 107	3 - 112
1	61	LYS	LYS	LEU	LEU	K	K	1 - 129	1 - 129
2	61	LYS	LYS	LEU	LEU	M	M	1 - 129	1 - 129
1	62	LYS	LYS	LEU	LEU	K	K	1 - 129	1 - 129
2	62	LYS	LYS	LEU	LEU	O	O	1 - 129	1 - 129
1	63	LYS	LYS	LEU	LEU	K	K	1 - 129	1 - 129
2	63	LYS	LYS	LEU	LEU	Q	Q	1 - 129	1 - 129
1	64	SER	SER	ASN	ASN	L	L	0 - 105	4 - 110
2	64	SER	SER	ASN	ASN	N	N	0 - 105	4 - 110
1	65	GLY	GLY	LYS	LYS	L	L	-1 - 106	3 - 111
2	65	GLY	GLY	LYS	LYS	P	P	-1 - 106	3 - 111
1	66	GLY	GLY	LYS	LYS	L	L	-1 - 108	3 - 113
2	66	GLY	GLY	LYS	LYS	R	R	-1 - 108	3 - 113
1	67	LYS	LYS	LEU	LEU	M	M	1 - 129	1 - 129
2	67	LYS	LYS	LEU	LEU	O	O	1 - 129	1 - 129
1	68	LYS	LYS	LEU	LEU	M	M	1 - 129	1 - 129
2	68	LYS	LYS	LEU	LEU	Q	Q	1 - 129	1 - 129
1	69	SER	SER	ASN	ASN	N	N	0 - 105	4 - 110
2	69	SER	SER	ASN	ASN	P	P	0 - 105	4 - 110
1	70	SER	SER	ASN	ASN	N	N	0 - 105	4 - 110
2	70	SER	SER	ASN	ASN	R	R	0 - 105	4 - 110
1	71	LYS	LYS	LEU	LEU	O	O	1 - 129	1 - 129
2	71	LYS	LYS	LEU	LEU	Q	Q	1 - 129	1 - 129
1	72	GLY	GLY	LYS	LYS	P	P	-1 - 106	3 - 111
2	72	GLY	GLY	LYS	LYS	R	R	-1 - 106	3 - 111

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72

Components

#1: Protein

A C E G I K M O Q
Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV

Details:

Mass: 14331.160 Da / Num. of mol.: 9 / Fragment: UNP residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme

#2: Protein

B D F H J L N P R
OBody AM1L10

Details:

Mass: 12313.108 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Gene: aspS / Plasmid: pProEx Htb / Production host: Escherichia coli (E. coli) / Strain (production host): DH5[alpha]

#3: Chemical

A-201 A-202 C-201 C-202 D-202 D-203 E-201 E-202 G-201 G-202 I-201 I-202 K-201 L-202 M-201 M-202 O-201 Q-201
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Details:

Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₃H₈O₃

#4: Chemical

B-201 D-201 F-201 H-201 J-201 L-201 N-201 P-201 R-201
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES

Details:

Mass: 238.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM

#5: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 2576 / Source method: isolated from a natural source / Formula: H₂O

• Has protein modification: Y

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.89 ų/Da / Density % sol: 57.41 %
• Crystal grow: Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 ; Details: 0.2 M HEPES, 9% MPEG5000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Type: SSRL / Wavelength: 0.95666 Å
• Detector: Type: MAR / Detector: CCD / Date: Nov 16, 2008; Details: flat collimating Rh coated mirror, toroidal focusing mirror
• Radiation: Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.95666 Å / Relative weight: 1
• Reflection: Redundancy: 14.3 % / Av σ(I) over netI: 7.3 / Number: 2883971 / R_sym value: 0.064 / D res high: 1.947 Å / D res low: 148.421 Å / Num. obs: 201770 / % possible obs: 99

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	Rmerge(I) obs	Rsym value	Redundancy
6.16	29.76	98.9	1	0.03	0.03	14
4.35	6.16	100	1	0.033	0.033	14.6
3.55	4.35	100	1	0.037	0.037	14.7
3.08	3.55	100	1	0.048	0.048	14.7
2.75	3.08	100	1	0.071	0.071	14.9
2.51	2.75	99.7	1	0.101	0.101	15
2.33	2.51	99.8	1	0.146	0.146	14.8
2.18	2.33	99.5	1	0.206	0.206	14.4
2.05	2.18	99.1	1	0.308	0.308	14
1.95	2.05	95.3	1	0.483	0.483	12.4

• Reflection: Resolution: 1.95→29.765 Å / Num. obs: 201770

Phasing

• Phasing: Method: molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	29.76 Å
Translation	2.5 Å	29.76 Å

Processing

Software

Name	Version	Classification	NB
XSCALE		data scaling
PHASER	2.3.0	phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29.765 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.952 / WR_factor R_free: 0.222 / WR_factor R_work: 0.1931 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8217 / SU B: 3.312 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1617 / SU R_free: 0.1436 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.2283	10150	5 %	RANDOM
Rwork	0.1992	-	-	-
obs	0.2007	201523	98.83 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 103.18 Ų / B_iso mean: 34.7894 Ų / B_iso min: 19.12 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.26 Å2	0 Å2	0 Å2
2-	-	-0.19 Å2	0 Å2
3-	-	-	0.45 Å2

Refinement step

Cycle: LAST / Resolution: 1.95→29.765 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16276	0	243	2576	19095

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.019	16940
X-RAY DIFFRACTION	r_angle_refined_deg	1.401	1.935	22960
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.509	5	2099
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.555	23.223	726
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.624	15	2718
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.071	15	126
X-RAY DIFFRACTION	r_chiral_restr	0.137	0.2	2513
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	12648

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: INTERATOMIC DISTANCE / Weight: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms
1	1	A	205	0.04
1	2	C	205	0.04
2	1	A	206	0.04
2	2	E	206	0.04
3	1	A	198	0.04
3	2	G	198	0.04
4	1	A	206	0.04
4	2	I	206	0.04
5	1	A	205	0.03
5	2	K	205	0.03
6	1	A	207	0.04
6	2	M	207	0.04
7	1	A	206	0.04
7	2	O	206	0.04
8	1	A	204	0.04
8	2	Q	204	0.04
9	1	B	116	0.01
9	2	D	116	0.01
10	1	B	116	0.09
10	2	F	116	0.09
11	1	B	106	0.01
11	2	H	106	0.01
12	1	B	113	0.11
12	2	J	113	0.11
13	1	B	116	0.12
13	2	L	116	0.12
14	1	B	110	0.01
14	2	N	110	0.01
15	1	B	112	0.01
15	2	P	112	0.01
16	1	B	114
16	2	R	114
17	1	C	207
17	2	E	207
18	1	C	199
18	2	G	199
19	1	C	206
19	2	I	206
20	1	C	205
20	2	K	205
21	1	C	206
21	2	M	206
22	1	C	204
22	2	O	204
23	1	C	205
23	2	Q	205
24	1	D	113
24	2	F	113
25	1	D	106
25	2	H	106
26	1	D	115	0.13
26	2	J	115	0.13
27	1	D	113	0.08
27	2	L	113	0.08
28	1	D	109	0.07
28	2	N	109	0.07
29	1	D	113	0.07
29	2	P	113	0.07
30	1	D	113	0.07
30	2	R	113	0.07
31	1	E	203
31	2	G	203
32	1	E	208
32	2	I	208
33	1	E	204
33	2	K	204
34	1	E	207
34	2	M	207
35	1	E	205
35	2	O	205
36	1	E	210
36	2	Q	210
37	1	F	105
37	2	H	105
38	1	F	114	0.11
38	2	J	114	0.11
39	1	F	115	0.08
39	2	L	115	0.08
40	1	F	108
40	2	N	108
41	1	F	111	0.01
41	2	P	111	0.01
42	1	F	112
42	2	R	112
43	1	G	199
43	2	I	199
44	1	G	196
44	2	K	196
45	1	G	200
45	2	M	200
46	1	G	198
46	2	O	198
47	1	G	201
47	2	Q	201
48	1	H	105
48	2	J	105
49	1	H	105
49	2	L	105
50	1	H	103
50	2	N	103
51	1	H	103	0.01
51	2	P	103	0.01
52	1	H	105
52	2	R	105
53	1	I	204
53	2	K	204
54	1	I	206
54	2	M	206
55	1	I	205
55	2	O	205
56	1	I	207
56	2	Q	207
57	1	J	114	0.07
57	2	L	114	0.07
58	1	J	108	0.08
58	2	N	108	0.08
59	1	J	110	0.08
59	2	P	110	0.08
60	1	J	113	0.11
60	2	R	113	0.11
61	1	K	204
61	2	M	204
62	1	K	203
62	2	O	203
63	1	K	204
63	2	Q	204
64	1	L	109	0.08
64	2	N	109	0.08
65	1	L	111	0.08
65	2	P	111	0.08
66	1	L	115	0.08
66	2	R	115	0.08
67	1	M	207
67	2	O	207
68	1	M	204
68	2	Q	204
69	1	N	110
69	2	P	110
70	1	N	111
70	2	R	111
71	1	O	204
71	2	Q	204
72	1	P	109	0.01
72	2	R	109	0.01

LS refinement shell

Resolution: 1.95→1.997 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.278	673	-
Rwork	0.245	12451	-
all	-	13124	-
obs	-	-	90.33 %