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- PDB-5cod: Bovine heart complex I membrane domain -

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Basic information

Entry
Database: PDB / ID: 5cod
TitleBovine heart complex I membrane domain
Components
  • (NADH-ubiquinone oxidoreductase chain ...) x 2
  • (Unknown structure) x 11
  • SDAP
KeywordsOXIDOREDUCTASE / Animals / Cattle / Electron Transport Complex I / Mitochondria / Heart / Models / Molecular / Protein Structure / Tertiary / Protein Subunits
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.74 Å
AuthorsZhu, J. / Hirst, J. / King, M.S. / Yu, M. / Leslie, A.G.W. / Klipcan, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure of subcomplex I beta of mammalian respiratory complex I leads to new supernumerary subunit assignments.
Authors: Zhu, J. / King, M.S. / Yu, M. / Klipcan, L. / Leslie, A.G. / Hirst, J.
History
DepositionJul 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L1: NADH-ubiquinone oxidoreductase chain 5
M1: NADH-ubiquinone oxidoreductase chain 4
f1: Unknown structure
g1: Unknown structure
h1: Unknown structure
i1: Unknown structure
j1: Unknown structure
k1: Unknown structure
l1: Unknown structure
U1: SDAP
n1: Unknown structure
o1: Unknown structure
p1: Unknown structure
s1: Unknown structure
t1: Unknown structure
u1: Unknown structure
v1: Unknown structure
w1: Unknown structure
BA: Unknown structure
L2: NADH-ubiquinone oxidoreductase chain 5
M2: NADH-ubiquinone oxidoreductase chain 4
f2: Unknown structure
g2: Unknown structure
h2: Unknown structure
i2: Unknown structure
j2: Unknown structure
k2: Unknown structure
l2: Unknown structure
U2: SDAP
n2: Unknown structure
o2: Unknown structure
p2: Unknown structure
s2: Unknown structure
t2: Unknown structure
u2: Unknown structure
v2: Unknown structure
w2: Unknown structure
BB: Unknown structure
L3: NADH-ubiquinone oxidoreductase chain 5
M3: NADH-ubiquinone oxidoreductase chain 4
f3: Unknown structure
g3: Unknown structure
h3: Unknown structure
i3: Unknown structure
j3: Unknown structure
k3: Unknown structure
l3: Unknown structure
U3: SDAP
n3: Unknown structure
o3: Unknown structure
p3: Unknown structure
s3: Unknown structure
t3: Unknown structure
u3: Unknown structure
v3: Unknown structure
w3: Unknown structure
BC: Unknown structure
L4: NADH-ubiquinone oxidoreductase chain 5
M4: NADH-ubiquinone oxidoreductase chain 4
f4: Unknown structure
g4: Unknown structure
h4: Unknown structure
i4: Unknown structure
j4: Unknown structure
k4: Unknown structure
l4: Unknown structure
U4: SDAP
n4: Unknown structure
o4: Unknown structure
p4: Unknown structure
s4: Unknown structure
t4: Unknown structure
u4: Unknown structure
v4: Unknown structure
w4: Unknown structure
BD: Unknown structure
L5: NADH-ubiquinone oxidoreductase chain 5
M5: NADH-ubiquinone oxidoreductase chain 4
f5: Unknown structure
g5: Unknown structure
h5: Unknown structure
i5: Unknown structure
j5: Unknown structure
k5: Unknown structure
l5: Unknown structure
U5: SDAP
n5: Unknown structure
o5: Unknown structure
p5: Unknown structure
s5: Unknown structure
t5: Unknown structure
u5: Unknown structure
v5: Unknown structure
w5: Unknown structure
BE: Unknown structure
L6: NADH-ubiquinone oxidoreductase chain 5
M6: NADH-ubiquinone oxidoreductase chain 4
f6: Unknown structure
g6: Unknown structure
h6: Unknown structure
i6: Unknown structure
j6: Unknown structure
k6: Unknown structure
l6: Unknown structure
U6: SDAP
n6: Unknown structure
o6: Unknown structure
p6: Unknown structure
s6: Unknown structure
t6: Unknown structure
u6: Unknown structure
v6: Unknown structure
w6: Unknown structure
BF: Unknown structure


Theoretical massNumber of molelcules
Total (without water)894,124114
Polymers894,124114
Non-polymers00
Water0
1
L1: NADH-ubiquinone oxidoreductase chain 5
M1: NADH-ubiquinone oxidoreductase chain 4
f1: Unknown structure
g1: Unknown structure
h1: Unknown structure
i1: Unknown structure
j1: Unknown structure
k1: Unknown structure
l1: Unknown structure
U1: SDAP
n1: Unknown structure
o1: Unknown structure
p1: Unknown structure
s1: Unknown structure
t1: Unknown structure
u1: Unknown structure
v1: Unknown structure
w1: Unknown structure
BA: Unknown structure


Theoretical massNumber of molelcules
Total (without water)149,02119
Polymers149,02119
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L2: NADH-ubiquinone oxidoreductase chain 5
M2: NADH-ubiquinone oxidoreductase chain 4
f2: Unknown structure
g2: Unknown structure
h2: Unknown structure
i2: Unknown structure
j2: Unknown structure
k2: Unknown structure
l2: Unknown structure
U2: SDAP
n2: Unknown structure
o2: Unknown structure
p2: Unknown structure
s2: Unknown structure
t2: Unknown structure
u2: Unknown structure
v2: Unknown structure
w2: Unknown structure
BB: Unknown structure


Theoretical massNumber of molelcules
Total (without water)149,02119
Polymers149,02119
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
L3: NADH-ubiquinone oxidoreductase chain 5
M3: NADH-ubiquinone oxidoreductase chain 4
f3: Unknown structure
g3: Unknown structure
h3: Unknown structure
i3: Unknown structure
j3: Unknown structure
k3: Unknown structure
l3: Unknown structure
U3: SDAP
n3: Unknown structure
o3: Unknown structure
p3: Unknown structure
s3: Unknown structure
t3: Unknown structure
u3: Unknown structure
v3: Unknown structure
w3: Unknown structure
BC: Unknown structure


Theoretical massNumber of molelcules
Total (without water)149,02119
Polymers149,02119
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
L4: NADH-ubiquinone oxidoreductase chain 5
M4: NADH-ubiquinone oxidoreductase chain 4
f4: Unknown structure
g4: Unknown structure
h4: Unknown structure
i4: Unknown structure
j4: Unknown structure
k4: Unknown structure
l4: Unknown structure
U4: SDAP
n4: Unknown structure
o4: Unknown structure
p4: Unknown structure
s4: Unknown structure
t4: Unknown structure
u4: Unknown structure
v4: Unknown structure
w4: Unknown structure
BD: Unknown structure


Theoretical massNumber of molelcules
Total (without water)149,02119
Polymers149,02119
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
L5: NADH-ubiquinone oxidoreductase chain 5
M5: NADH-ubiquinone oxidoreductase chain 4
f5: Unknown structure
g5: Unknown structure
h5: Unknown structure
i5: Unknown structure
j5: Unknown structure
k5: Unknown structure
l5: Unknown structure
U5: SDAP
n5: Unknown structure
o5: Unknown structure
p5: Unknown structure
s5: Unknown structure
t5: Unknown structure
u5: Unknown structure
v5: Unknown structure
w5: Unknown structure
BE: Unknown structure


Theoretical massNumber of molelcules
Total (without water)149,02119
Polymers149,02119
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
L6: NADH-ubiquinone oxidoreductase chain 5
M6: NADH-ubiquinone oxidoreductase chain 4
f6: Unknown structure
g6: Unknown structure
h6: Unknown structure
i6: Unknown structure
j6: Unknown structure
k6: Unknown structure
l6: Unknown structure
U6: SDAP
n6: Unknown structure
o6: Unknown structure
p6: Unknown structure
s6: Unknown structure
t6: Unknown structure
u6: Unknown structure
v6: Unknown structure
w6: Unknown structure
BF: Unknown structure


Theoretical massNumber of molelcules
Total (without water)149,02119
Polymers149,02119
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)244.832, 251.414, 412.034
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
12
22
32
42
52
62
72
82
92
102
112
122
13
23
33
43
53
63
14
24
34
44
54
64
74
84
94
104
114
124
134
144
154
164
174
184
194
204
214
224
234
244
254
264
274
284
294
304
314
324
334
344
354
364
374
384
394
404
414
424
434
444
454
464
474
484
494
504
514
524
534
544
15
25
35
45
55
65
75
85
95
105
115
125
16
26
36
46
56
66
76
86
96
106
116
126
17
27
37
47
57
67
77
87
97
107
117
127

NCS domain segments:

Beg auth comp-ID: UNK / Beg label comp-ID: UNK / End auth comp-ID: UNK / End label comp-ID: UNK

Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111chain 'BA'BAS528 - 5461 - 19
121chain 'BA'BAS548 - 56221 - 35
131chain 'BA'BAS571 - 58637 - 52
141chain 'BA'BAS1588 - 162554 - 91
151chain 'BA'BAS1632 - 163893 - 99
161chain 'BA'BAS1642 - 1648101 - 107
171chain 'BA'BAS1651 - 1658109 - 116
181chain 'BA'BAS1660 - 1667118 - 125
191chain 'BA'BAS1669 - 1687127 - 145
2101chain 'BB'BBLA528 - 5461 - 19
2111chain 'BB'BBLA548 - 56221 - 35
2121chain 'BB'BBLA571 - 58637 - 52
2131chain 'BB'BBLA1588 - 162554 - 91
2141chain 'BB'BBLA1632 - 163893 - 99
2151chain 'BB'BBLA1642 - 1648101 - 107
2161chain 'BB'BBLA1651 - 1658109 - 116
2171chain 'BB'BBLA1660 - 1667118 - 125
2181chain 'BB'BBLA1669 - 1687127 - 145
3191chain 'BC'BCEB528 - 5461 - 19
3201chain 'BC'BCEB548 - 56221 - 35
3211chain 'BC'BCEB571 - 58637 - 52
3221chain 'BC'BCEB1588 - 162554 - 91
3231chain 'BC'BCEB1632 - 163893 - 99
3241chain 'BC'BCEB1642 - 1648101 - 107
3251chain 'BC'BCEB1651 - 1658109 - 116
3261chain 'BC'BCEB1660 - 1667118 - 125
3271chain 'BC'BCEB1669 - 1687127 - 145
4281chain 'BD'BDXB528 - 5461 - 19
4291chain 'BD'BDXB548 - 56221 - 35
4301chain 'BD'BDXB571 - 58637 - 52
4311chain 'BD'BDXB1588 - 162554 - 91
4321chain 'BD'BDXB1632 - 163893 - 99
4331chain 'BD'BDXB1642 - 1648101 - 107
4341chain 'BD'BDXB1651 - 1658109 - 116
4351chain 'BD'BDXB1660 - 1667118 - 125
4361chain 'BD'BDXB1669 - 1687127 - 145
5371chain 'BE'BEQC528 - 5461 - 19
5381chain 'BE'BEQC548 - 56221 - 35
5391chain 'BE'BEQC571 - 58637 - 52
5401chain 'BE'BEQC1588 - 162554 - 91
5411chain 'BE'BEQC1632 - 163893 - 99
5421chain 'BE'BEQC1642 - 1648101 - 107
5431chain 'BE'BEQC1651 - 1658109 - 116
5441chain 'BE'BEQC1660 - 1667118 - 125
5451chain 'BE'BEQC1669 - 1687127 - 145
6461chain 'BF'BFJD528 - 5461 - 19
6471chain 'BF'BFJD548 - 56221 - 35
6481chain 'BF'BFJD571 - 58637 - 52
6491chain 'BF'BFJD1588 - 162554 - 91
6501chain 'BF'BFJD1632 - 163893 - 99
6511chain 'BF'BFJD1642 - 1648101 - 107
6521chain 'BF'BFJD1651 - 1658109 - 116
6531chain 'BF'BFJD1660 - 1667118 - 125
6541chain 'BF'BFJD1669 - 1687127 - 145
1552chain 'L1'L1A5 - 212 - 18
1562chain 'L1'L1A28 - 21320 - 205
1572chain 'L1'L1A216 - 357207 - 348
1582chain 'L1'L1A363 - 399350 - 386
1592chain 'L1'L1A489 - 512469 - 492
2602chain 'L2'L2T5 - 212 - 18
2612chain 'L2'L2T28 - 21320 - 205
2622chain 'L2'L2T216 - 357207 - 348
2632chain 'L2'L2T363 - 399350 - 386
2642chain 'L2'L2T489 - 512469 - 492
3652chain 'L3'L3MA5 - 212 - 18
3662chain 'L3'L3MA28 - 21320 - 205
3672chain 'L3'L3MA216 - 357207 - 348
3682chain 'L3'L3MA363 - 399350 - 386
3692chain 'L3'L3MA489 - 512469 - 492
4702chain 'L4'L4FB5 - 212 - 18
4712chain 'L4'L4FB28 - 21320 - 205
4722chain 'L4'L4FB216 - 357207 - 348
4732chain 'L4'L4FB363 - 399350 - 386
4742chain 'L4'L4FB489 - 512469 - 492
5752chain 'L5'L5YB5 - 212 - 18
5762chain 'L5'L5YB28 - 21320 - 205
5772chain 'L5'L5YB216 - 357207 - 348
5782chain 'L5'L5YB363 - 399350 - 386
5792chain 'L5'L5YB489 - 512469 - 492
6802chain 'L6'L6RC5 - 212 - 18
6812chain 'L6'L6RC28 - 21320 - 205
6822chain 'L6'L6RC216 - 357207 - 348
6832chain 'L6'L6RC363 - 399350 - 386
6842chain 'L6'L6RC489 - 512469 - 492
7852chain 'M1'M1B20 - 3618 - 34
7862chain 'M1'M1B43 - 22841 - 226
7872chain 'M1'M1B231 - 372229 - 370
7882chain 'M1'M1B378 - 414376 - 412
7892chain 'M1'M1B431 - 454415 - 438
8902chain 'M2'M2U20 - 3618 - 34
8912chain 'M2'M2U43 - 22841 - 226
8922chain 'M2'M2U231 - 372229 - 370
8932chain 'M2'M2U378 - 414376 - 412
8942chain 'M2'M2U431 - 454415 - 438
9952chain 'M3'M3NA20 - 3618 - 34
9962chain 'M3'M3NA43 - 22841 - 226
9972chain 'M3'M3NA231 - 372229 - 370
9982chain 'M3'M3NA378 - 414376 - 412
9992chain 'M3'M3NA431 - 454415 - 438
101002chain 'M4'M4GB20 - 3618 - 34
101012chain 'M4'M4GB43 - 22841 - 226
101022chain 'M4'M4GB231 - 372229 - 370
101032chain 'M4'M4GB378 - 414376 - 412
101042chain 'M4'M4GB431 - 454415 - 438
111052chain 'M5'M5ZB20 - 3618 - 34
111062chain 'M5'M5ZB43 - 22841 - 226
111072chain 'M5'M5ZB231 - 372229 - 370
111082chain 'M5'M5ZB378 - 414376 - 412
111092chain 'M5'M5ZB431 - 454415 - 438
121102chain 'M6'M6SC20 - 3618 - 34
121112chain 'M6'M6SC43 - 22841 - 226
121122chain 'M6'M6SC231 - 372229 - 370
121132chain 'M6'M6SC378 - 414376 - 412
121142chain 'M6'M6SC431 - 454415 - 438
11153chain 'U1'U1J8 - 811 - 74
21163chain 'U2'U2CA8 - 811 - 74
31173chain 'U3'U3VA8 - 811 - 74
41183chain 'U4'U4OB8 - 811 - 74
51193chain 'U5'U5HC8 - 811 - 74
61203chain 'U6'U6AD8 - 811 - 74
11214chain 'f1'f1C5 - 295 - 29
21224chain 'f2'f2V5 - 295 - 29
31234chain 'f3'f3OA5 - 295 - 29
41244chain 'f4'f4HB5 - 295 - 29
51254chain 'f5'f5AC5 - 295 - 29
61264chain 'f6'f6TC5 - 295 - 29
71274chain 'h1'h1E5 - 295 - 29
81284chain 'h2'h2X5 - 295 - 29
91294chain 'h3'h3QA5 - 295 - 29
101304chain 'h4'h4JB5 - 295 - 29
111314chain 'h5'h5CC5 - 295 - 29
121324chain 'h6'h6VC5 - 295 - 29
131334chain 'i1'i1F5 - 295 - 29
141344chain 'i2'i2Y5 - 295 - 29
151354chain 'i3'i3RA5 - 295 - 29
161364chain 'i4'i4KB5 - 295 - 29
171374chain 'i5'i5DC5 - 295 - 29
181384chain 'i6'i6WC5 - 295 - 29
191394chain 'j1'j1G3 - 273 - 27
201404chain 'j2'j2Z3 - 273 - 27
211414chain 'j3'j3SA3 - 273 - 27
221424chain 'j4'j4LB3 - 273 - 27
231434chain 'j5'j5EC3 - 273 - 27
241444chain 'j6'j6XC3 - 273 - 27
251454chain 'k1'k1H3 - 273 - 27
261464chain 'k2'k2AA3 - 273 - 27
271474chain 'k3'k3TA3 - 273 - 27
281484chain 'k4'k4MB3 - 273 - 27
291494chain 'k5'k5FC3 - 273 - 27
301504chain 'k6'k6YC3 - 273 - 27
311514chain 'p1'p1M3 - 273 - 27
321524chain 'p2'p2FA3 - 273 - 27
331534chain 'p3'p3YA3 - 273 - 27
341544chain 'p4'p4RB3 - 273 - 27
351554chain 'p5'p5KC3 - 273 - 27
361564chain 'p6'p6DD3 - 273 - 27
371574chain 's1's1N3 - 273 - 27
381584chain 's2's2GA3 - 273 - 27
391594chain 's3's3ZA3 - 273 - 27
401604chain 's4's4SB3 - 273 - 27
411614chain 's5's5LC3 - 273 - 27
421624chain 's6's6ED3 - 273 - 27
431634chain 'v1'v1Q7 - 317 - 31
441644chain 'v2'v2JA7 - 317 - 31
451654chain 'v3'v3CB7 - 317 - 31
461664chain 'v4'v4VB7 - 317 - 31
471674chain 'v5'v5OC7 - 317 - 31
481684chain 'v6'v6HD7 - 317 - 31
491694chain 'w1'w1R2 - 262 - 26
501704chain 'w2'w2KA2 - 262 - 26
511714chain 'w3'w3DB2 - 262 - 26
521724chain 'w4'w4WB2 - 262 - 26
531734chain 'w5'w5PC2 - 262 - 26
541744chain 'w6'w6ID2 - 262 - 26
11755chain 'g1'g1D3 - 213 - 21
21765chain 'g2'g2W3 - 213 - 21
31775chain 'g3'g3PA3 - 213 - 21
41785chain 'g4'g4IB3 - 213 - 21
51795chain 'g5'g5BC3 - 213 - 21
61805chain 'g6'g6UC3 - 213 - 21
71815chain 'o1'o1L2 - 202 - 20
81825chain 'o2'o2EA2 - 202 - 20
91835chain 'o3'o3XA2 - 202 - 20
101845chain 'o4'o4QB2 - 202 - 20
111855chain 'o5'o5JC2 - 202 - 20
121865chain 'o6'o6CD2 - 202 - 20
11876chain 'l1'l1I12 - 231 - 12
21886chain 'l2'l2BA12 - 231 - 12
31896chain 'l3'l3UA12 - 231 - 12
41906chain 'l4'l4NB12 - 231 - 12
51916chain 'l5'l5GC12 - 231 - 12
61926chain 'l6'l6ZC12 - 231 - 12
71936chain 'u1'u1P3 - 143 - 14
81946chain 'u2'u2IA3 - 143 - 14
91956chain 'u3'u3BB3 - 143 - 14
101966chain 'u4'u4UB3 - 143 - 14
111976chain 'u5'u5NC3 - 143 - 14
121986chain 'u6'u6GD3 - 143 - 14
11997chain 'n1'n1K4 - 584 - 58
22007chain 'n2'n2DA4 - 584 - 58
32017chain 'n3'n3WA4 - 584 - 58
42027chain 'n4'n4PB4 - 584 - 58
52037chain 'n5'n5IC4 - 584 - 58
62047chain 'n6'n6BD4 - 584 - 58
72057chain 't1't1O2 - 562 - 56
82067chain 't2't2HA2 - 562 - 56
92077chain 't3't3AB2 - 562 - 56
102087chain 't4't4TB2 - 562 - 56
112097chain 't5't5MC2 - 562 - 56
122107chain 't6't6FD2 - 562 - 56

NCS ensembles :
ID
1
2
3
4
5
6
7

-
Components

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NADH-ubiquinone oxidoreductase chain ... , 2 types, 12 molecules L1L2L3L4L5L6M1M2M3M4M5M6

#1: Protein
NADH-ubiquinone oxidoreductase chain 5 / ND5 of bovine complex I


Mass: 51591.719 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
#2: Protein
NADH-ubiquinone oxidoreductase chain 4 / ND4 of bovine complex I


Mass: 39081.152 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)

-
Protein/peptide , 8 types, 78 molecules f1h1i1f2h2i2f3h3i3f4h4i4f5h5i5f6h6i6g1g2g3g4g5g6j1k1p1s1j2k2...

#3: Protein/peptide
Unknown structure


Mass: 2571.161 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
#4: Protein/peptide
Unknown structure


Mass: 1890.321 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
#5: Protein/peptide ...
Unknown structure


Mass: 2400.951 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
#6: Protein/peptide
Unknown structure


Mass: 1124.378 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
#9: Protein/peptide
Unknown structure


Mass: 1805.216 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
#11: Protein/peptide
Unknown structure


Mass: 1294.587 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
#12: Protein/peptide
Unknown structure


Mass: 2741.370 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
#13: Protein/peptide
Unknown structure


Mass: 2315.846 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)

-
Protein , 4 types, 24 molecules U1U2U3U4U5U6n1n2n3n4n5n6t1t2t3t4t5t6BABBBCBDBEBF

#7: Protein
SDAP


Mass: 7507.245 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
#8: Protein
Unknown structure


Mass: 5039.203 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
#10: Protein
Unknown structure


Mass: 4868.993 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
#14: Protein
Unknown structure


Mass: 12443.330 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: Tris-HCl, magnesium chloride, sodium chloride, PEG 3350, n-Dodecyl beta-D-maltoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 6.74→49.4 Å / Num. obs: 44280 / % possible obs: 97.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 495.710145503 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.4
Reflection shellResolution: 6.8→7.2 Å / Rmerge(I) obs: 1.27

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Processing

Software
NameVersionClassification
XDSdata reduction
MOSFLMdata reduction
PHENIX1.9_1692refinement
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4uq8

4uq8


Resolution: 6.74→41.6873198321 Å / SU ML: 1.73175135834 / Cross valid method: FREE R-VALUE / σ(F): 1.3388412943 / Phase error: 49.9623021003
RfactorNum. reflection% reflection
Rfree0.434647338379 2222 5.03409683047 %
Rwork0.424796773066 41917 -
obs0.425205947788 44139 97.1582654634 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100 Å2
Refinement stepCycle: LAST / Resolution: 6.74→41.6873198321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48030 0 0 0 48030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011729072265947838
X-RAY DIFFRACTIONf_angle_d2.1766345570466666
X-RAY DIFFRACTIONf_chiral_restr0.1124141969959606
X-RAY DIFFRACTIONf_plane_restr0.009454059401339414
X-RAY DIFFRACTIONf_dihedral_angle_d5.879876933959414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.7387-6.88460.4765913053211300.4541908537492320X-RAY DIFFRACTION87.3751783167
6.8846-7.0440.4409014674231400.4529147302782625X-RAY DIFFRACTION99.353215954
7.044-7.21930.478487780711380.4408705188312663X-RAY DIFFRACTION99.0102509721
7.2193-7.41340.4328250305631380.4429524024622632X-RAY DIFFRACTION99.0701001431
7.4134-7.63030.4705688845181430.4541199650822654X-RAY DIFFRACTION98.8688582538
7.6303-7.8750.4363499093791370.4667652353032615X-RAY DIFFRACTION98.9928057554
7.875-8.15450.407108040751370.4341636001822634X-RAY DIFFRACTION98.506932101
8.1545-8.47830.4133200537541310.4049025767992640X-RAY DIFFRACTION98.4019886364
8.4783-8.86070.3795458041841450.3937692019032630X-RAY DIFFRACTION98.6140724947
8.8607-9.32290.4007843984241420.3870703478162663X-RAY DIFFRACTION98.872047938
9.3229-9.89970.3565942829061440.3539872336762642X-RAY DIFFRACTION98.7593052109
9.8997-10.65230.3251682934631370.3416300606392695X-RAY DIFFRACTION98.7447698745
10.6523-11.70270.4176303307561440.3609966786282645X-RAY DIFFRACTION97.7910238429
11.7027-13.34720.4193036965431400.3959811405612651X-RAY DIFFRACTION97.1796657382
13.3472-16.63630.4897821761141450.4501080645972718X-RAY DIFFRACTION98.4525447043
16.6363-41.68810.5264388870461310.523674890132490X-RAY DIFFRACTION87.1632856668

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