PDB-4b7x: Crystal structure of hypothetical protein PA1648 from Pseudomonas...

Basic information

• Entry: Database: PDB / ID: 4b7x
• Title: Crystal structure of hypothetical protein PA1648 from Pseudomonas aeruginosa.
• Components: PROBABLE OXIDOREDUCTASE
• Keywords: OXIDOREDUCTASE

Function / homology

Function:

oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / nucleotide binding

Domain/homology:

Medium-chain dehydrogenase/reductase / Oxidoreductase, N-terminal domain / N-terminal domain of oxidoreductase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta

Component:

NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Probable oxidoreductase

• Biological species: PSEUDOMONAS AERUGINOSA PAO1 (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
• Authors: Alphey, M.S. / McMahon, S.A. / Duthie, F. / Naismith, J.H.
• Citation: Journal: Acta Crystallogr.,Sect.F / Year: 2013; Title: The Aeropath Project Targeting Pseudomonas Aeruginosa: Crystallographic Studies for Assessment of Potential Targets in Early-Stage Drug Discovery; Authors: Moynie, L. / Schnell, R. / Mcmahon, S.A. / Sandalova, T. / Boulkerou, W.A. / Schmidberger, J.W. / Alphey, M.S. / Cukier, C. / Duthie, F. / Kopec, J. / Liu, H. / Jacewicz, A. / Hunter, W.N. / Naismith, J.H. / Schneider, G.

History

Deposition	Aug 24, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 23, 2013	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PROBABLE OXIDOREDUCTASE

B: PROBABLE OXIDOREDUCTASE

C: PROBABLE OXIDOREDUCTASE

D: PROBABLE OXIDOREDUCTASE

E: PROBABLE OXIDOREDUCTASE

F: PROBABLE OXIDOREDUCTASE

G: PROBABLE OXIDOREDUCTASE

H: PROBABLE OXIDOREDUCTASE

I: PROBABLE OXIDOREDUCTASE

J: PROBABLE OXIDOREDUCTASE

K: PROBABLE OXIDOREDUCTASE

L: PROBABLE OXIDOREDUCTASE

hetero molecules

Summary:

• 445 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	444,938	24
Polymers	436,017	12
Non-polymers	8,921	12
Water	11,782	654

1

G: PROBABLE OXIDOREDUCTASE

H: PROBABLE OXIDOREDUCTASE

hetero molecules

Summary:

• defined by software
• 74.2 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	74,156	4
Polymers	72,669	2
Non-polymers	1,487	2
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	5270 Å2
ΔGint	-31.2 kcal/mol
Surface area	26110 Å2
Method	PISA

2

C: PROBABLE OXIDOREDUCTASE

D: PROBABLE OXIDOREDUCTASE

hetero molecules

Summary:

• defined by software
• 74.2 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	74,156	4
Polymers	72,669	2
Non-polymers	1,487	2
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	5270 Å2
ΔGint	-30.5 kcal/mol
Surface area	26550 Å2
Method	PISA

3

K: PROBABLE OXIDOREDUCTASE

L: PROBABLE OXIDOREDUCTASE

hetero molecules

Summary:

• defined by software
• 74.2 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	74,156	4
Polymers	72,669	2
Non-polymers	1,487	2
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	5140 Å2
ΔGint	-32 kcal/mol
Surface area	26200 Å2
Method	PISA

4

A: PROBABLE OXIDOREDUCTASE

B: PROBABLE OXIDOREDUCTASE

hetero molecules

Summary:

• defined by software
• 74.2 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	74,156	4
Polymers	72,669	2
Non-polymers	1,487	2
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	5270 Å2
ΔGint	-29.6 kcal/mol
Surface area	25860 Å2
Method	PISA

5

I: PROBABLE OXIDOREDUCTASE

J: PROBABLE OXIDOREDUCTASE

hetero molecules

Summary:

• defined by software
• 74.2 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	74,156	4
Polymers	72,669	2
Non-polymers	1,487	2
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	5120 Å2
ΔGint	-29.5 kcal/mol
Surface area	23680 Å2
Method	PISA

6

E: PROBABLE OXIDOREDUCTASE

F: PROBABLE OXIDOREDUCTASE

hetero molecules

Summary:

• defined by software
• 74.2 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	74,156	4
Polymers	72,669	2
Non-polymers	1,487	2
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	5330 Å2
ΔGint	-28.5 kcal/mol
Surface area	26260 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	169.260, 175.970, 182.170
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
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	A
2	8	I
1	9	A
2	9	J
1	10	A
2	10	K
1	11	A
2	11	L
1	12	B
2	12	C
1	13	B
2	13	D
1	14	B
2	14	E
1	15	B
2	15	F
1	16	B
2	16	G
1	17	B
2	17	H
1	18	B
2	18	I
1	19	B
2	19	J
1	20	B
2	20	K
1	21	B
2	21	L
1	22	C
2	22	D
1	23	C
2	23	E
1	24	C
2	24	F
1	25	C
2	25	G
1	26	C
2	26	H
1	27	C
2	27	I
1	28	C
2	28	J
1	29	C
2	29	K
1	30	C
2	30	L
1	31	D
2	31	E
1	32	D
2	32	F
1	33	D
2	33	G
1	34	D
2	34	H
1	35	D
2	35	I
1	36	D
2	36	J
1	37	D
2	37	K
1	38	D
2	38	L
1	39	E
2	39	F
1	40	E
2	40	G
1	41	E
2	41	H
1	42	E
2	42	I
1	43	E
2	43	J
1	44	E
2	44	K
1	45	E
2	45	L
1	46	F
2	46	G
1	47	F
2	47	H
1	48	F
2	48	I
1	49	F
2	49	J
1	50	F
2	50	K
1	51	F
2	51	L
1	52	G
2	52	H
1	53	G
2	53	I
1	54	G
2	54	J
1	55	G
2	55	K
1	56	G
2	56	L
1	57	H
2	57	I
1	58	H
2	58	J
1	59	H
2	59	K
1	60	H
2	60	L
1	61	I
2	61	J
1	62	I
2	62	K
1	63	I
2	63	L
1	64	J
2	64	K
1	65	J
2	65	L
1	66	K
2	66	L

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	GLN	GLN	VAL	VAL	A	A	4 - 334	6 - 336
2	1	GLN	GLN	VAL	VAL	B	B	4 - 334	6 - 336
1	2	ILE	ILE	VAL	VAL	A	A	5 - 334	7 - 336
2	2	ILE	ILE	VAL	VAL	C	C	5 - 334	7 - 336
1	3	GLN	GLN	VAL	VAL	A	A	4 - 334	6 - 336
2	3	GLN	GLN	VAL	VAL	D	D	4 - 334	6 - 336
1	4	GLN	GLN	VAL	VAL	A	A	4 - 334	6 - 336
2	4	GLN	GLN	VAL	VAL	E	E	4 - 334	6 - 336
1	5	GLN	GLN	VAL	VAL	A	A	4 - 334	6 - 336
2	5	GLN	GLN	VAL	VAL	F	F	4 - 334	6 - 336
1	6	GLN	GLN	LYS	LYS	A	A	4 - 333	6 - 335
2	6	GLN	GLN	LYS	LYS	G	G	4 - 333	6 - 335
1	7	GLN	GLN	VAL	VAL	A	A	4 - 334	6 - 336
2	7	GLN	GLN	VAL	VAL	H	H	4 - 334	6 - 336
1	8	GLY	GLY	VAL	VAL	A	A	99 - 331	101 - 333
2	8	ALA	ALA	VAL	VAL	I	I	51 - 331	53 - 333
1	9	ASN	ASN	LYS	LYS	A	A	6 - 333	8 - 335
2	9	ASN	ASN	LYS	LYS	J	J	6 - 333	8 - 335
1	10	GLN	GLN	LYS	LYS	A	A	4 - 333	6 - 335
2	10	GLN	GLN	LYS	LYS	K	K	4 - 333	6 - 335
1	11	GLN	GLN	VAL	VAL	A	A	4 - 334	6 - 336
2	11	GLN	GLN	VAL	VAL	L	L	4 - 334	6 - 336
1	12	ILE	ILE	VAL	VAL	B	B	5 - 334	7 - 336
2	12	ILE	ILE	VAL	VAL	C	C	5 - 334	7 - 336
1	13	GLN	GLN	VAL	VAL	B	B	4 - 334	6 - 336
2	13	GLN	GLN	VAL	VAL	D	D	4 - 334	6 - 336
1	14	GLN	GLN	VAL	VAL	B	B	4 - 334	6 - 336
2	14	GLN	GLN	VAL	VAL	E	E	4 - 334	6 - 336
1	15	GLN	GLN	VAL	VAL	B	B	4 - 334	6 - 336
2	15	GLN	GLN	VAL	VAL	F	F	4 - 334	6 - 336
1	16	GLN	GLN	LYS	LYS	B	B	4 - 333	6 - 335
2	16	GLN	GLN	LYS	LYS	G	G	4 - 333	6 - 335
1	17	GLN	GLN	VAL	VAL	B	B	4 - 334	6 - 336
2	17	GLN	GLN	VAL	VAL	H	H	4 - 334	6 - 336
1	18	GLY	GLY	VAL	VAL	B	B	99 - 331	101 - 333
2	18	ALA	ALA	VAL	VAL	I	I	51 - 331	53 - 333
1	19	ASN	ASN	VAL	VAL	B	B	6 - 334	8 - 336
2	19	ASN	ASN	VAL	VAL	J	J	6 - 334	8 - 336
1	20	GLN	GLN	LYS	LYS	B	B	4 - 333	6 - 335
2	20	GLN	GLN	LYS	LYS	K	K	4 - 333	6 - 335
1	21	GLN	GLN	LYS	LYS	B	B	4 - 333	6 - 335
2	21	GLN	GLN	LYS	LYS	L	L	4 - 333	6 - 335
1	22	ILE	ILE	VAL	VAL	C	C	5 - 334	7 - 336
2	22	ILE	ILE	VAL	VAL	D	D	5 - 334	7 - 336
1	23	ILE	ILE	VAL	VAL	C	C	5 - 334	7 - 336
2	23	ILE	ILE	VAL	VAL	E	E	5 - 334	7 - 336
1	24	ILE	ILE	VAL	VAL	C	C	5 - 334	7 - 336
2	24	ILE	ILE	VAL	VAL	F	F	5 - 334	7 - 336
1	25	ILE	ILE	LYS	LYS	C	C	5 - 333	7 - 335
2	25	ILE	ILE	LYS	LYS	G	G	5 - 333	7 - 335
1	26	ILE	ILE	VAL	VAL	C	C	5 - 334	7 - 336
2	26	ILE	ILE	VAL	VAL	H	H	5 - 334	7 - 336
1	27	GLY	GLY	VAL	VAL	C	C	99 - 331	101 - 333
2	27	ALA	ALA	VAL	VAL	I	I	51 - 331	53 - 333
1	28	ASN	ASN	VAL	VAL	C	C	6 - 334	8 - 336
2	28	ASN	ASN	VAL	VAL	J	J	6 - 334	8 - 336
1	29	ILE	ILE	VAL	VAL	C	C	5 - 334	7 - 336
2	29	ILE	ILE	VAL	VAL	K	K	5 - 334	7 - 336
1	30	ILE	ILE	VAL	VAL	C	C	5 - 334	7 - 336
2	30	ILE	ILE	VAL	VAL	L	L	5 - 334	7 - 336
1	31	GLN	GLN	VAL	VAL	D	D	4 - 334	6 - 336
2	31	GLN	GLN	VAL	VAL	E	E	4 - 334	6 - 336
1	32	GLN	GLN	VAL	VAL	D	D	4 - 334	6 - 336
2	32	GLN	GLN	VAL	VAL	F	F	4 - 334	6 - 336
1	33	GLN	GLN	LYS	LYS	D	D	4 - 333	6 - 335
2	33	GLN	GLN	LYS	LYS	G	G	4 - 333	6 - 335
1	34	GLN	GLN	VAL	VAL	D	D	4 - 334	6 - 336
2	34	GLN	GLN	VAL	VAL	H	H	4 - 334	6 - 336
1	35	GLY	GLY	VAL	VAL	D	D	99 - 331	101 - 333
2	35	ALA	ALA	VAL	VAL	I	I	51 - 331	53 - 333
1	36	ASN	ASN	VAL	VAL	D	D	6 - 334	8 - 336
2	36	ASN	ASN	VAL	VAL	J	J	6 - 334	8 - 336
1	37	GLN	GLN	VAL	VAL	D	D	4 - 334	6 - 336
2	37	GLN	GLN	VAL	VAL	K	K	4 - 334	6 - 336
1	38	GLN	GLN	VAL	VAL	D	D	4 - 334	6 - 336
2	38	GLN	GLN	VAL	VAL	L	L	4 - 334	6 - 336
1	39	GLN	GLN	VAL	VAL	E	E	4 - 334	6 - 336
2	39	GLN	GLN	VAL	VAL	F	F	4 - 334	6 - 336
1	40	GLN	GLN	LYS	LYS	E	E	4 - 333	6 - 335
2	40	GLN	GLN	LYS	LYS	G	G	4 - 333	6 - 335
1	41	GLN	GLN	VAL	VAL	E	E	4 - 334	6 - 336
2	41	GLN	GLN	VAL	VAL	H	H	4 - 334	6 - 336
1	42	GLY	GLY	VAL	VAL	E	E	99 - 331	101 - 333
2	42	ALA	ALA	VAL	VAL	I	I	51 - 331	53 - 333
1	43	ASN	ASN	VAL	VAL	E	E	6 - 334	8 - 336
2	43	ASN	ASN	VAL	VAL	J	J	6 - 334	8 - 336
1	44	GLN	GLN	LYS	LYS	E	E	4 - 333	6 - 335
2	44	GLN	GLN	LYS	LYS	K	K	4 - 333	6 - 335
1	45	GLN	GLN	LYS	LYS	E	E	4 - 333	6 - 335
2	45	GLN	GLN	LYS	LYS	L	L	4 - 333	6 - 335
1	46	GLN	GLN	LYS	LYS	F	F	4 - 333	6 - 335
2	46	GLN	GLN	LYS	LYS	G	G	4 - 333	6 - 335
1	47	GLN	GLN	VAL	VAL	F	F	4 - 334	6 - 336
2	47	GLN	GLN	VAL	VAL	H	H	4 - 334	6 - 336
1	48	GLY	GLY	VAL	VAL	F	F	99 - 331	101 - 333
2	48	ALA	ALA	VAL	VAL	I	I	51 - 331	53 - 333
1	49	ASN	ASN	VAL	VAL	F	F	6 - 334	8 - 336
2	49	ASN	ASN	VAL	VAL	J	J	6 - 334	8 - 336
1	50	GLN	GLN	LYS	LYS	F	F	4 - 333	6 - 335
2	50	GLN	GLN	LYS	LYS	K	K	4 - 333	6 - 335
1	51	GLN	GLN	LYS	LYS	F	F	4 - 333	6 - 335
2	51	GLN	GLN	LYS	LYS	L	L	4 - 333	6 - 335
1	52	GLN	GLN	LYS	LYS	G	G	4 - 333	6 - 335
2	52	GLN	GLN	LYS	LYS	H	H	4 - 333	6 - 335
1	53	GLY	GLY	VAL	VAL	G	G	99 - 331	101 - 333
2	53	ALA	ALA	VAL	VAL	I	I	51 - 331	53 - 333
1	54	ASN	ASN	LYS	LYS	G	G	6 - 333	8 - 335
2	54	ASN	ASN	LYS	LYS	J	J	6 - 333	8 - 335
1	55	GLN	GLN	LYS	LYS	G	G	4 - 333	6 - 335
2	55	GLN	GLN	LYS	LYS	K	K	4 - 333	6 - 335
1	56	GLN	GLN	LYS	LYS	G	G	4 - 333	6 - 335
2	56	GLN	GLN	LYS	LYS	L	L	4 - 333	6 - 335
1	57	GLY	GLY	VAL	VAL	H	H	99 - 331	101 - 333
2	57	ALA	ALA	VAL	VAL	I	I	51 - 331	53 - 333
1	58	ASN	ASN	VAL	VAL	H	H	6 - 334	8 - 336
2	58	ASN	ASN	VAL	VAL	J	J	6 - 334	8 - 336
1	59	GLN	GLN	VAL	VAL	H	H	4 - 334	6 - 336
2	59	GLN	GLN	VAL	VAL	K	K	4 - 334	6 - 336
1	60	GLN	GLN	VAL	VAL	H	H	4 - 334	6 - 336
2	60	GLN	GLN	VAL	VAL	L	L	4 - 334	6 - 336
1	61	ALA	ALA	VAL	VAL	I	I	51 - 331	53 - 333
2	61	GLY	GLY	VAL	VAL	J	J	99 - 331	101 - 333
1	62	ALA	ALA	VAL	VAL	I	I	51 - 331	53 - 333
2	62	GLY	GLY	VAL	VAL	K	K	99 - 331	101 - 333
1	63	ALA	ALA	VAL	VAL	I	I	51 - 331	53 - 333
2	63	GLY	GLY	VAL	VAL	L	L	99 - 331	101 - 333
1	64	ASN	ASN	LYS	LYS	J	J	6 - 333	8 - 335
2	64	ASN	ASN	LYS	LYS	K	K	6 - 333	8 - 335
1	65	ASN	ASN	VAL	VAL	J	J	6 - 334	8 - 336
2	65	ASN	ASN	VAL	VAL	L	L	6 - 334	8 - 336
1	66	GLN	GLN	VAL	VAL	K	K	4 - 334	6 - 336
2	66	GLN	GLN	VAL	VAL	L	L	4 - 334	6 - 336

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

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.504, 0.6546, -0.5634), (0.6482, -0.1444, -0.7477), (-0.5708, -0.7421, -0.3515)	-53.96, 57.72, 19.13
2	given	(0.548, 0.8299, 0.1042), (-0.6212, 0.4873, -0.6137), (-0.5601, 0.2716, 0.7826)	-12.94, 23.96, 32.57
3	given	(-0.375, -0.3133, -0.8722), (0.8691, 0.2076, -0.449), (0.3217, -0.9267, 0.1942)	-50.59, 20.51, -1.286
4	given	(-0.997, 0.02012, -0.07484), (-0.07441, 0.02101, 0.997), (0.02163, 0.9996, -0.01945)	-47.63, 43.71, -45.62
5	given	(0.4243, -0.5329, 0.7321), (-0.6155, -0.7627, -0.1985), (0.6642, -0.3664, -0.6516)	23.13, 56.26, 30.74
6	given	(0.3447, 0.3178, 0.8833), (0.2843, -0.9321, 0.2244), (0.8946, 0.1737, -0.4116)	4.373, 46.32, -24.78
7	given	(-0.5029, -0.8564, -0.1165), (-0.5057, 0.1822, 0.8433), (-0.701, 0.483, -0.5247)	-14.31, 72.46, -9.609
8	given	(0.5386, -0.0141, -0.8424), (0.3896, 0.8907, 0.2342), (0.747, -0.4544, 0.4853)	-25.158, 61.0383, 68.4607
9	given	(-0.422, 0.8425, 0.3347), (-0.2862, 0.2265, -0.931), (-0.8602, -0.4887, 0.1456)	-37.54, -19.51, -35.8
10	given	(-0.535, -0.02962, 0.8443), (0.7188, -0.541, 0.4365), (0.4439, 0.8405, 0.3107)	1.116, 101.3, 30.88
11	given	(0.4935, -0.8155, -0.3025), (-0.8051, -0.5599, 0.1958), (-0.329, 0.1469, -0.9328)	-4.86, 15.92, -66.75

Components

#1: Protein

A B C D E F G H I J K L
PROBABLE OXIDOREDUCTASE / PA1648

Details:

Mass: 36334.738 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q9I377

#2: Chemical

A-400 B-400 C-400 D-400 E-400 F-400 G-400 H-400 I-400 J-400 K-400 L-400
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE

Details:

Mass: 743.405 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 654 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 3.13 ų/Da / Density % sol: 60.6 % / Description: NONE
• Crystal grow: pH: 6.5 ; Details: 0.9 M NA CITRATE, 0.1 M MES PH 6.5, 0.1 M MGSO4, 10 % GLYCEROL

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793
• Detector: Type: ADSC CCD / Detector: CCD / Date: Dec 10, 2010
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9793 Å / Relative weight: 1
• Reflection: Resolution: 2.2→56.42 Å / Num. obs: 273854 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.9 % / B_iso Wilson estimate: 33.8 Ų / R_merge(I) obs: 0.1 / Net I/σ(I): 13
• Reflection shell: Resolution: 2.2→2.32 Å / Redundancy: 8.1 % / R_merge(I) obs: 0.68 / Mean I/σ(I) obs: 3 / % possible all: 100

Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B7C

4b7c

Resolution: 2.2→56.42 Å / Cor.coef. F_o:F_c: 0.926 / Cor.coef. F_o:F_c free: 0.902 / SU B: 6.267 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.2759	13809	5.08 %	RANDOM
Rwork	0.237	-	-	-
obs	0.239	273580	99.767 %	-

• Solvent computation: Ion probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 45.071 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.781 Å2	0 Å2	0 Å2
2-	-	-1.393 Å2	0 Å2
3-	-	-	2.175 Å2

Refinement step

Cycle: LAST / Resolution: 2.2→56.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28978	0	576	654	30208

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.02	30137
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.245	2.01	40788
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.632	5	3777
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.577	23.807	1266
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.243	15	5019
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.258	15	217
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	4493
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	22671
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	13952
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.309	0.2	20336
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.126	0.2	1087
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	2.259	4.495	30137
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.587	6.695	40788
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	6.275	13.705	10279
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.985	21.531	34760
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	423	0.04
1	2	B	423	0.04
2	1	A	406	0.04
2	2	C	406	0.04
3	1	A	410	0.04
3	2	D	410	0.04
4	1	A	417	0.06
4	2	E	417	0.06
5	1	A	409	0.09
5	2	F	409	0.09
6	1	A	384	0.06
6	2	G	384	0.06
7	1	A	408	0.06
7	2	H	408	0.06
8	1	A	279	0.05
8	2	I	279	0.05
9	1	A	414	0.08
9	2	J	414	0.08
10	1	A	344	0.07
10	2	K	344	0.07
11	1	A	406	0.04
11	2	L	406	0.04
12	1	B	412	0.03
12	2	C	412	0.03
13	1	B	412	0.03
13	2	D	412	0.03
14	1	B	419	0.06
14	2	E	419	0.06
15	1	B	416	0.08
15	2	F	416	0.08
16	1	B	388	0.08
16	2	G	388	0.08
17	1	B	417	0.08
17	2	H	417	0.08
18	1	B	281	0.05
18	2	I	281	0.05
19	1	B	415	0.08
19	2	J	415	0.08
20	1	B	346	0.07
20	2	K	346	0.07
21	1	B	406	0.04
21	2	L	406	0.04
22	1	C	407	0.06
22	2	D	407	0.06
23	1	C	408	0.03
23	2	E	408	0.03
24	1	C	399	0.08
24	2	F	399	0.08
25	1	C	391	0.07
25	2	G	391	0.07
26	1	C	407	0.05
26	2	H	407	0.05
27	1	C	278	0.05
27	2	I	278	0.05
28	1	C	402	0.05
28	2	J	402	0.05
29	1	C	344	0.08
29	2	K	344	0.08
30	1	C	399	0.04
30	2	L	399	0.04
31	1	D	413	0.06
31	2	E	413	0.06
32	1	D	408	0.08
32	2	F	408	0.08
33	1	D	386	0.07
33	2	G	386	0.07
34	1	D	406	0.08
34	2	H	406	0.08
35	1	D	278	0.07
35	2	I	278	0.07
36	1	D	413	0.07
36	2	J	413	0.07
37	1	D	339	0.08
37	2	K	339	0.08
38	1	D	413	0.06
38	2	L	413	0.06
39	1	E	410	0.09
39	2	F	410	0.09
40	1	E	393	0.08
40	2	G	393	0.08
41	1	E	416	0.06
41	2	H	416	0.06
42	1	E	276	0.05
42	2	I	276	0.05
43	1	E	408	0.08
43	2	J	408	0.08
44	1	E	339	0.09
44	2	K	339	0.09
45	1	E	402	0.06
45	2	L	402	0.06
46	1	F	380	0.1
46	2	G	380	0.1
47	1	F	410	0.1
47	2	H	410	0.1
48	1	F	275	0.07
48	2	I	275	0.07
49	1	F	404	0.09
49	2	J	404	0.09
50	1	F	342	0.11
50	2	K	342	0.11
51	1	F	407	0.09
51	2	L	407	0.09
52	1	G	390	0.08
52	2	H	390	0.08
53	1	G	276	0.08
53	2	I	276	0.08
54	1	G	387	0.07
54	2	J	387	0.07
55	1	G	327	0.1
55	2	K	327	0.1
56	1	G	381	0.08
56	2	L	381	0.08
57	1	H	285	0.09
57	2	I	285	0.09
58	1	H	403	0.07
58	2	J	403	0.07
59	1	H	338	0.1
59	2	K	338	0.1
60	1	H	399	0.07
60	2	L	399	0.07
61	1	I	282	0.05
61	2	J	282	0.05
62	1	I	228	0.06
62	2	K	228	0.06
63	1	I	275	0.07
63	2	L	275	0.07
64	1	J	337	0.11
64	2	K	337	0.11
65	1	J	403	0.09
65	2	L	403	0.09
66	1	K	345	0.07
66	2	L	345	0.07

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.341	1010	-
Rwork	0.3	18322	-
obs	-	-	99.964 %