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- PDB-2xq1: Crystal structure of peroxisomal catalase from the yeast Hansenul... -

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Basic information

Entry
Database: PDB / ID: 2xq1
TitleCrystal structure of peroxisomal catalase from the yeast Hansenula polymorpha
ComponentsPEROXISOMAL CATALASE
KeywordsOXIDOREDUCTASE / HYDROGEN PEROXIDE DETOXIFICATION / PTS1
Function / homology
Function and homology information


catalase / catalase activity / peroxisomal matrix / hydrogen peroxide catabolic process / response to hydrogen peroxide / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. ...Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Peroxisomal catalase
Similarity search - Component
Biological speciesPICHIA ANGUSTA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPenya-Soler, E. / Vega, M.C. / Wilmanns, M. / Williams, C.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structural Features of Peroxisomal Catalase from the Yeast Hansenula Polymorpha
Authors: Penya-Soler, E. / Vega, M.C. / Wilmanns, M. / Williams, C.P.
History
DepositionAug 31, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2011Group: Database references / Version format compliance
Revision 1.2Mar 28, 2012Group: Other
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEROXISOMAL CATALASE
B: PEROXISOMAL CATALASE
C: PEROXISOMAL CATALASE
D: PEROXISOMAL CATALASE
E: PEROXISOMAL CATALASE
F: PEROXISOMAL CATALASE
G: PEROXISOMAL CATALASE
H: PEROXISOMAL CATALASE
I: PEROXISOMAL CATALASE
J: PEROXISOMAL CATALASE
K: PEROXISOMAL CATALASE
L: PEROXISOMAL CATALASE
M: PEROXISOMAL CATALASE
N: PEROXISOMAL CATALASE
O: PEROXISOMAL CATALASE
P: PEROXISOMAL CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)937,80431
Polymers928,55716
Non-polymers9,24715
Water1,17165
1
M: PEROXISOMAL CATALASE
N: PEROXISOMAL CATALASE
O: PEROXISOMAL CATALASE
P: PEROXISOMAL CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,6058
Polymers232,1394
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46050 Å2
ΔGint-334.6 kcal/mol
Surface area61930 Å2
MethodPISA
2
A: PEROXISOMAL CATALASE
B: PEROXISOMAL CATALASE
C: PEROXISOMAL CATALASE
D: PEROXISOMAL CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,9897
Polymers232,1394
Non-polymers1,8493
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44660 Å2
ΔGint-315.5 kcal/mol
Surface area62550 Å2
MethodPISA
3
I: PEROXISOMAL CATALASE
J: PEROXISOMAL CATALASE
K: PEROXISOMAL CATALASE
L: PEROXISOMAL CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,6058
Polymers232,1394
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45710 Å2
ΔGint-330 kcal/mol
Surface area62000 Å2
MethodPISA
4
E: PEROXISOMAL CATALASE
F: PEROXISOMAL CATALASE
G: PEROXISOMAL CATALASE
H: PEROXISOMAL CATALASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,6058
Polymers232,1394
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45600 Å2
ΔGint-327 kcal/mol
Surface area61950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.520, 196.680, 170.850
Angle α, β, γ (deg.)90.00, 92.85, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A8 - 400
2111B8 - 400
3111C8 - 400
4111D8 - 400
5111E8 - 400
6111F8 - 400
7111G8 - 400
8111H8 - 400
9111I8 - 400
10111J8 - 400
11111K8 - 400
12111L8 - 400
13111M8 - 400
14111N8 - 400
15111O8 - 400
16111P8 - 400
1214A402 - 408
2214B402 - 408
3214C402 - 408
4214D402 - 408
5214E402 - 408
6214F402 - 408
7214G402 - 408
8214H402 - 408
9214I402 - 408
10214J402 - 408
11214K402 - 408
12214L402 - 408
13214M402 - 408
14214N402 - 408
15214O402 - 408
16214P402 - 408
1314A414 - 417
2314B414 - 417
3314C414 - 417
4314D414 - 417
5314E414 - 417
6314F414 - 417
7314G414 - 417
8314H414 - 417
9314I414 - 417
10314J414 - 417
11314K414 - 417
12314L414 - 417
13314M414 - 417
14314N414 - 417
15314O414 - 417
16314P414 - 417
1411A419 - 491
2411B419 - 491
3411C419 - 491
4411D419 - 491
5411E419 - 491
6411F419 - 491
7411G419 - 491
8411H419 - 491
9411I419 - 491
10411J419 - 491
11411K419 - 491
12411L419 - 491
13411M419 - 491
14411N419 - 491
15411O419 - 491
16411P419 - 491
1514A493 - 501
2514B493 - 501
3514C493 - 501
4514D493 - 501
5514E493 - 501
6514F493 - 501
7514G493 - 501
8514H493 - 501
9514I493 - 501
10514J493 - 501
11514K493 - 501
12514L493 - 501
13514M493 - 501
14514N493 - 501
15514O493 - 501
16514P493 - 501

NCS oper:
IDCodeMatrixVector
1given(0.8977, -0.4395, 0.03236), (-0.4393, -0.8983, -0.01357), (0.03503, -0.02035, -0.9994)-13.57, -57.91, 13.87
2given(-0.9961, 0.02037, 0.08536), (0.02767, -0.8501, 0.5259), (0.08328, 0.5262, 0.8463)-24.51, -54.51, 16.64
3given(-0.9028, 0.4119, -0.1234), (0.4129, 0.7505, -0.516), (-0.1199, -0.5169, -0.8476)-11.06, 1.706, -3.285
4given(-0.9991, -0.04124, -0.06943), (-0.02911, 0.8051, -0.5924), (0.03002, -0.5917, -0.8056)40.07, -4.032, -14.51
5given(-0.8823, -0.4133, 0.2253), (0.4664, -0.702, 0.5382), (-0.06425, 0.5799, 0.8121)23.51, -71.88, 29.62
6given(0.9968, 0.01294, -0.07929), (0.01894, -0.997, 0.0754), (-0.07808, -0.07666, -0.994)-65.58, -57.9, 5.915
7given(0.8817, 0.4496, -0.1433), (-0.4572, 0.889, -0.02384), (0.1167, 0.08655, 0.9894)-46.61, 22.94, 5.825
8given(-0.9992, -0.03239, 0.02342), (-0.03202, 0.2977, -0.9541), (0.02393, -0.9541, -0.2985)27, 40.79, 52.85
9given(-0.8769, -0.1935, 0.4401), (0.4777, -0.2474, 0.843), (-0.05424, 0.9494, 0.3094)-6.47, -106.6, -38.9
10given(0.996, -0.0441, -0.07777), (0.01736, -0.7579, 0.6521), (-0.08771, -0.6508, -0.7541)-45.17, -60.49, 85.45
11given(0.8785, 0.2726, -0.3923), (-0.4603, 0.7025, -0.5428), (0.1276, 0.6574, 0.7426)-23.71, 15.83, -72.76
12given(1, 0.007655, 0.001141), (-0.005565, 0.8137, -0.5813), (-0.005378, 0.5813, 0.8137)13.04, -4.399, -80.84
13given(0.8973, -0.3315, 0.2914), (-0.4391, -0.7381, 0.5122), (0.04529, -0.5876, -0.8079)-3.358, -58.86, 95.08
14given(-0.9967, 0.06045, 0.05395), (0.02678, -0.3826, 0.9235), (0.07647, 0.9219, 0.3798)-44.31, -93.12, -52.77
15given(-0.9048, 0.2557, -0.3406), (0.4107, 0.312, -0.8567), (-0.1128, -0.915, -0.3873)-14.72, 45.54, 65.82
16given(0.9026, -0.43, 0.01821), (-0.4296, -0.9028, -0.0211), (0.02551, 0.01122, -0.9996)-12.76, -57.9, 14.44
17given(-0.9961, 0.02044, 0.08547), (0.02767, -0.8502, 0.5258), (0.08341, 0.5261, 0.8463)-24.51, -54.51, 16.64
18given(-0.9029, 0.4118, -0.1235), (0.4129, 0.7505, -0.5161), (-0.1198, -0.5169, -0.8476)-11.06, 1.707, -3.285
19given(-0.9991, -0.04141, -0.00695), (-0.02924, 0.8051, -0.5924), (0.03013, -0.5917, -0.8056)40.07, -4.025, -14.52
20given(-0.8823, -0.4133, 0.2254), (0.4664, -0.702, 0.5382), (-0.06415, 0.5799, 0.8121)23.51, -71.88, 29.62
21given(0.9828, 0.01632, -0.1841), (0.02906, -0.9973, 0.06673), (-0.1825, -0.07093, -0.9806)-62.11, -58.54, 14.07
22given(0.8816, 0.4496, -0.1434), (-0.4573, 0.889, -0.02368), (0.1169, 0.08646, 0.9894)-46.61, 22.95, 5.813
23given(-0.9992, -0.03241, 0.02344), (-0.03204, 0.2977, -0.9541), (0.02394, -0.9541, -0.2985)27, 40.8, 52.85
24given(-0.8769, -0.1935, 0.4401), (0.4777, -0.2474, 0.843), (-0.05421, 0.9494, 0.3094)-6.471, -106.6, -38.9
25given(0.996, -0.04414, -0.07783), (0.01737, -0.758, 0.6521), (-0.08777, -0.6508, -0.7541)-45.16, -60.49, 85.46
26given(0.8786, 0.2726, -0.3922), (-0.4603, 0.7025, -0.5428), (0.1276, 0.6574, 0.7426)-23.71, 15.83, -72.76
27given(1, 0.007633, 0.00119), (-0.005519, 0.8136, -0.5813), (-0.005405, 0.5813, 0.8137)13.04, -4.398, -80.84
28given(0.8911, -0.3245, 0.3171), (-0.4481, -0.7388, 0.5034), (0.0709, -0.5907, -0.8038)-6.564, -57.82, 94.8
29given(-0.9967, 0.06051, 0.05395), (0.02675, -0.3827, 0.9235), (0.07652, 0.9219, 0.3798)-44.31, -93.13, -52.77
30given(-0.9048, 0.2556, -0.3406), (0.4107, 0.312, -0.8567), (-0.1127, -0.915, -0.3873)-14.72, 45.54, 65.81
31given(0.8203, -0.572, -0.003532), (-0.5718, -0.8202, 0.01523), (-0.01161, -0.01048, -0.9999)-13.81, -57.67, 13.86
32given(-0.9914, -0.01537, 0.1298), (0.07817, -0.8656, 0.4945), (0.1048, 0.5005, 0.8594)-23.94, -54.53, 17
33given(-0.903, 0.4115, -0.1236), (0.4126, 0.7506, -0.5161), (-0.1196, -0.517, -0.8476)-11.06, 1.704, -3.284
34given(-0.9952, 0.04706, -0.08613), (0.08882, 0.8052, -0.5863), (0.04177, -0.5911, -0.8055)44.92, -9.387, -14.98
35given(-0.8823, -0.4131, 0.2255), (0.4663, -0.7021, 0.5382), (-0.064, 0.58, 0.8121)23.52, -71.89, 29.61
36given(0.9954, -0.08605, -0.04117), (-0.0776, -0.9815, 0.1753), (-0.05549, -0.1713, -0.9837)67.64, -54.57, 3.375
37given(0.7795, 0.605, -0.1622), (-0.619, 0.7837, -0.05156), (0.09593, 0.1406, 0.9854)-33.76, 27.85, 9.502
38given(-0.9992, -0.03263, 0.02361), (-0.03227, 0.2978, -0.9541), (0.0241, -0.9541, -0.2987)26.99, 40.79, 52.86
39given(-0.8769, -0.1934, 0.4401), (0.4776, -0.2476, 0.843), (-0.05404, 0.9494, 0.3095)-6.466, -106.6, -38.91
40given(0.996, -0.04396, -0.0779), (0.01755, -0.7579, 0.6521), (-0.08771, -0.6509, -0.7541)-45.17, -60.5, 85.45
41given(0.8786, 0.2726, -0.3922), (-0.4603, 0.7025, -0.5429), (0.1276, 0.6575, 0.7426)-23.72, 15.84, -72.76
42given(1, 0.007718, 0.001505), (-0.005404, 0.8136, -0.5814), (-0.005712, 0.5813, 0.8136)13.02, -4.394, -80.84
43given(0.8565, -0.4143, 0.308), (-0.5141, -0.6304, 0.5816), (-0.04676, -0.6565, -0.7529)-0.2735, -73.97, 92.79
44given(-0.9967, 0.06069, 0.05402), (0.02675, -0.3828, 0.9235), (0.07673, 0.9219, 0.3799)-44.31, -93.12, -52.76
45given(-0.7782, 0.2287, -0.5849), (0.6203, 0.1349, -0.7727), (-0.09777, -0.9641, -0.2468)18.93, 55.12, 53.8
46given(0.8973, -0.4401, 0.03389), (-0.4399, -0.898, -0.01458), (0.03685, -0.0182, -0.9993)-13.63, -57.9, 13.9
47given(-0.9961, 0.02028, 0.08544), (0.02779, -0.8501, 0.5258), (0.0833, 0.5262, 0.8463)-24.51, -54.51, 16.64
48given(-0.9028, 0.4118, -0.1235), (0.4129, 0.7504, -0.5161), (-0.1199, -0.517, -0.8475)-11.06, 1.702, -3.289
49given(-0.9991, -0.04123, -0.006842), (-0.02916, 0.805, -0.5926), (0.02994, -0.5919, -0.8055)40.08, -4.035, -14.52
50given(-0.8822, -0.4134, 0.2254), (0.4665, -0.702, 0.5382), (-0.06425, 0.5799, 0.8121)23.51, -71.89, 29.62
51given(0.9968, 0.01329, -0.07876), (0.01925, -0.997, 0.07544), (-0.07752, -0.07671, -0.994)-65.59, -57.92, 5.893
52given(0.8813, 0.4503, -0.1435), (-0.4579, 0.8887, -0.02313), (0.1171, 0.08608, 0.9894)-46.55, 22.96, 5.774
53given(-0.9992, -0.03231, 0.02334), (-0.03192, 0.2978, -0.9541), (0.02388, -0.9541, -0.2985)27.01, 40.79, 52.86
54given(-0.8768, -0.1935, 0.4402), (0.4778, -0.2474, 0.8429), (-0.05424, 0.9494, 0.3094)-6.473, -106.6, -38.9
55given(0.996, -0.04418, -0.07767), (0.01723, -0.7579, 0.6521), (-0.08768, -0.6508, -0.7541)-45.17, -60.49, 85.46
56given(0.8785, 0.2726, -0.3923), (-0.4604, 0.7025, -0.5428), (0.1276, 0.6574, 0.7426)-23.7, 15.83, -72.76
57given(1, 0.007704, 0.001082), (-0.005639, 0.8137, -0.5813), (-0.005359, 0.5813, 0.8137)13.05, -4.402, -80.84
58given(0.8971, -0.3314, 0.2921), (-0.4394, -0.7381, 0.512), (0.04594, -0.5877, -0.8078)-3.421, -58.85, 95.09
59given(-0.9967, 0.06034, 0.05405), (0.02692, -0.3825, 0.9236), (0.0764, 0.922, 0.3796)-44.3, -93.13, -52.76
60given(-0.9047, 0.2557, -0.3406), (0.4107, 0.312, -0.8567), (-0.1128, -0.915, -0.3873)-14.72, 45.54, 65.81
61given(0.8744, -0.4819, 0.05609), (-0.483, -0.8756, 0.005699), (0.04636, -0.03207, -0.9984)-13.56, -58.83, 14.84
62given(-0.9962, -0.04856, 0.0724), (0.07882, -0.8565, 0.5101), (0.03724, 0.5139, 0.8571)-24.48, -55.11, 17.4
63given(-0.8736, 0.4674, -0.1357), (0.4734, 0.7512, -0.46), (-0.113, -0.4661, -0.8775)-7.115, 0.7183, 1.459
64given(-0.9981, 0.03008, -0.05418), (0.05627, 0.8062, -0.589), (0.02595, -0.5909, -0.8063)45.47, -10.76, -14.02
65given(-0.8675, -0.461, 0.1869), (0.4881, -0.7168, 0.498), (-0.09563, 0.5232, 0.8468)21.37, -74.06, 33.11
66given(0.999, 0.0302, -0.03281), (0.03345, -0.9941, 0.1034), (-0.0295, -0.1044, -0.9941)-66.28, -58.23, 5.009
67given(0.8528, 0.4728, -0.2219), (-0.4841, 0.875, 0.003479), (0.1958, 0.1045, 0.9751)-43.82, 23.65, 3.176
68given(-0.9981, 0.01576, -0.0593), (0.06134, 0.2807, -0.9578), (0.001543, -0.9597, -0.2811)35.83, 35.52, 52.47
69given(-0.817, -0.3483, 0.4596), (0.5468, -0.2146, 0.8093), (-0.1832, 0.9125, 0.3658)-4.496, -109.1, -34.04
70given(0.9984, -0.05579, -0.007883), (-0.03503, -0.7243, 0.6886), (-0.04413, -0.6872, -0.7251)-48.51, -63.65, 85.47
71given(0.8258, 0.1981, -0.528), (-0.513, 0.6529, -0.5573), (0.2343, 0.7311, 0.6408)-8.553, 19.18, -65.08
72given(0.9996, -0.00531, -0.02892), (-0.01266, 0.8101, -0.5862), (0.02654, 0.5863, 0.8096)15.84, -4.014, -78.64
73given(0.8601, -0.3134, 0.4024), (-0.4879, -0.7358, 0.4696), (0.1489, -0.6003, -0.7858)-13.09, -57.19, 97.58
74given(-0.9969, 0.05267, 0.05913), (0.03059, -0.4326, 0.9011), (0.07304, 0.9, 0.4296)-44.68, -89.71, -53.75
75given(-0.9103, 0.2817, -0.3034), (0.3927, 0.3551, -0.8484), (-0.1313, -0.8914, -0.4338)-20.63, 43.54, 71.27

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Components

#1: Protein
PEROXISOMAL CATALASE


Mass: 58034.793 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) PICHIA ANGUSTA (fungus) / References: UniProt: P30263, catalase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.14 % / Description: NONE
Crystal growDetails: 0.2 M MAGNESIUM FORMATE, 20% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 11, 2009 / Details: DIAMOND (111), GE(220)
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.9→49.43 Å / Num. obs: 193014 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.9
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A4E

1a4e


Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.901 / SU B: 30.238 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22297 976 0.5 %RANDOM
Rwork0.19059 ---
obs0.19076 191418 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.516 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.01 Å2
2--0.03 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms63129 0 645 65 63839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02265955
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9790063
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39557828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4623.7753290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.695159898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.70715368
X-RAY DIFFRACTIONr_chiral_restr0.0960.29156
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02152440
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7761.539349
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.463263953
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.557326606
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6764.526110
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3731tight positional0.140.05
2B3731tight positional0.130.05
3C3731tight positional0.130.05
4D3731tight positional0.130.05
5E3731tight positional0.140.05
6F3731tight positional0.120.05
7G3731tight positional0.140.05
8H3731tight positional0.120.05
9I3731tight positional0.140.05
10J3731tight positional0.140.05
11K3731tight positional0.120.05
12L3731tight positional0.130.05
13M3731tight positional0.120.05
14N3731tight positional0.140.05
15O3731tight positional0.120.05
16P3731tight positional0.130.05
1A84medium positional0.670.5
2B84medium positional0.310.5
3C84medium positional0.370.5
4D84medium positional0.270.5
5E84medium positional0.460.5
6F84medium positional0.350.5
7G84medium positional0.390.5
8H84medium positional0.380.5
9I84medium positional0.370.5
10J84medium positional0.710.5
11K84medium positional0.350.5
12L84medium positional0.650.5
13M84medium positional0.310.5
14N84medium positional0.940.5
15O84medium positional0.490.5
16P84medium positional0.410.5
1A3731tight thermal0.780.5
2B3731tight thermal0.830.5
3C3731tight thermal0.710.5
4D3731tight thermal0.530.5
5E3731tight thermal0.610.5
6F3731tight thermal0.920.5
7G3731tight thermal0.790.5
8H3731tight thermal0.610.5
9I3731tight thermal0.530.5
10J3731tight thermal0.620.5
11K3731tight thermal0.60.5
12L3731tight thermal0.650.5
13M3731tight thermal0.790.5
14N3731tight thermal0.930.5
15O3731tight thermal0.620.5
16P3731tight thermal1.20.5
1A84medium thermal1.62
2B84medium thermal0.962
3C84medium thermal1.462
4D84medium thermal0.832
5E84medium thermal1.592
6F84medium thermal11.192
7G84medium thermal1.172
8H84medium thermal0.872
9I84medium thermal1.092
10J84medium thermal12
11K84medium thermal1.052
12L84medium thermal12
13M84medium thermal1.032
14N84medium thermal1.262
15O84medium thermal0.892
16P84medium thermal1.062
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 69 -
Rwork0.298 13850 -
obs--99.71 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
1-1.8063-28.853537.4675
2-9.289-50.278-1.0108
3-5.307-53.6374-5.0203
4-4.3599-38.6185-14.9562
5-30.8483-68.8782-3.8254
61.932-11.938113.8314
7-8.55455.791825.1828
8-30.6306-13.46222.389
9-20.5372-12.938212.2795
10-15.8227-9.1684-17.6019
11-23.6023-20.9006-12.1169
12-8.2699-15.5731-25.4341
138.10094.2294-26.505
14-24.5562-41.33219.3502
15-22.5188-34.158432.2483
16-9.0768-65.082940.5682
1750.0878-45.347914.6319
1853.3219-38.801123.0877
1940.9035-18.7988-15.0984
2036.6381-25.0465-21.6935
2148.7266-16.5855-37.6141
2254.10387.8823-37.369
2357.3647-9.2428-1.512
2463.0807-7.18766.4166
2543.56113.757813.6918
2667.7863-32.46338.1122
2767.293-49.4044-14.8961
2857.0681-61.309-20.9473
2952.8586-79.9007-7.6185
3036.709322.0517101.3485
3140.167532.8961104.6701
3217.639740.428888.6176
3327.016236.755577.329
3425.638221.096151.2902
3524.943513.656865.6977
3634.837814.798943.016
3739.055930.187528.0934
3858.295214.932259.3876
3947.290923.142161.5698
4041.408853.139170.5655
4149.862648.415172.2691
4232.616761.323574.4023
4315.729463.537555.2214
4454.03526.240183.4909
4545.7936-4.734380.7696
46-21.748613.93993.8378
47-17.89326.302584.6761
48-43.4953-8.48399.8555
49-11.49848.78881.4581
50-22.459370.80978.6932
51-31.248462.178596.8669
52-29.520129.898357.432
53-37.062629.3942101.8883
54-41.093438.2243104.3458
55-27.870138.8778120.9022
56-22.658322.1021133.8476
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 32
2X-RAY DIFFRACTION2A33 - 229
3X-RAY DIFFRACTION3A230 - 363
4X-RAY DIFFRACTION4A364 - 442
5X-RAY DIFFRACTION5A443 - 500
6X-RAY DIFFRACTION6B2 - 397
7X-RAY DIFFRACTION7B398 - 501
8X-RAY DIFFRACTION8C4 - 11
9X-RAY DIFFRACTION9C12 - 92
10X-RAY DIFFRACTION10C93 - 283
11X-RAY DIFFRACTION11C284 - 393
12X-RAY DIFFRACTION12C394 - 480
13X-RAY DIFFRACTION13C481 - 501
14X-RAY DIFFRACTION14D2 - 260
15X-RAY DIFFRACTION15D261 - 480
16X-RAY DIFFRACTION16D481 - 501
17X-RAY DIFFRACTION17E5 - 291
18X-RAY DIFFRACTION18E292 - 501
19X-RAY DIFFRACTION19F2 - 230
20X-RAY DIFFRACTION20F231 - 397
21X-RAY DIFFRACTION21F398 - 485
22X-RAY DIFFRACTION22F486 - 501
23X-RAY DIFFRACTION23G4 - 229
24X-RAY DIFFRACTION24G230 - 397
25X-RAY DIFFRACTION25G398 - 501
26X-RAY DIFFRACTION26H6 - 92
27X-RAY DIFFRACTION27H93 - 397
28X-RAY DIFFRACTION28H398 - 481
29X-RAY DIFFRACTION29H482 - 501
30X-RAY DIFFRACTION30I4 - 287
31X-RAY DIFFRACTION31I288 - 500
32X-RAY DIFFRACTION32J2 - 11
33X-RAY DIFFRACTION33J12 - 92
34X-RAY DIFFRACTION34J93 - 283
35X-RAY DIFFRACTION35J284 - 398
36X-RAY DIFFRACTION36J399 - 479
37X-RAY DIFFRACTION37J480 - 500
38X-RAY DIFFRACTION38K4 - 11
39X-RAY DIFFRACTION39K12 - 89
40X-RAY DIFFRACTION40K90 - 228
41X-RAY DIFFRACTION41K229 - 397
42X-RAY DIFFRACTION42K398 - 486
43X-RAY DIFFRACTION43K487 - 501
44X-RAY DIFFRACTION44L6 - 365
45X-RAY DIFFRACTION45L366 - 501
46X-RAY DIFFRACTION46M4 - 226
47X-RAY DIFFRACTION47M227 - 439
48X-RAY DIFFRACTION48M440 - 501
49X-RAY DIFFRACTION49N2 - 399
50X-RAY DIFFRACTION50N400 - 500
51X-RAY DIFFRACTION51O4 - 42
52X-RAY DIFFRACTION52O43 - 501
53X-RAY DIFFRACTION53P4 - 230
54X-RAY DIFFRACTION54P231 - 398
55X-RAY DIFFRACTION55P399 - 479
56X-RAY DIFFRACTION56P480 - 501

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