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- PDB-6fp6: Complex of human Cu,Zn SOD1 with the human copper chaperone for S... -

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Basic information

Entry
Database: PDB / ID: 6fp6
TitleComplex of human Cu,Zn SOD1 with the human copper chaperone for SOD1 in a compact conformation
Components
  • Copper chaperone for superoxide dismutase
  • Superoxide dismutase [Cu-Zn]
KeywordsMETAL BINDING PROTEIN / heterodimer / copper-chaperone / hSOD1 / protein maturation
Function / homology
Function and homology information


superoxide dismutase copper chaperone activity / action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth ...superoxide dismutase copper chaperone activity / action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide / regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / cellular response to potassium ion / retrograde axonal transport / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / response to copper ion / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / cellular response to ATP / negative regulation of reproductive process / negative regulation of developmental process / cellular response to cadmium ion / transmission of nerve impulse / protein-disulfide reductase activity / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of superoxide anion generation / axon cytoplasm / embryo implantation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of phagocytosis / response to amphetamine / thymus development / protein maturation / positive regulation of cytokine production / placenta development / regulation of mitochondrial membrane potential / determination of adult lifespan / locomotory behavior / response to nutrient levels / response to hydrogen peroxide / sensory perception of sound / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / regulation of blood pressure / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cellular response to oxidative stress / cytoplasmic vesicle / response to ethanol / spermatogenesis / gene expression / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / lysosome / positive regulation of MAPK cascade / positive regulation of apoptotic process / cadherin binding / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Superoxide dismutase, copper/zinc binding domain / Heavy metal-associated domain, HMA / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain ...Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Superoxide dismutase, copper/zinc binding domain / Heavy metal-associated domain, HMA / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PROPANOIC ACID / Copper chaperone for superoxide dismutase / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSala, F.A. / Wright, G.S.A. / Antonyuk, S.V. / Garratt, R.C. / Hasnain, S.S.
Funding support United Kingdom, Brazil, 5items
OrganizationGrant numberCountry
Motor Neurone Disease AssociationHasnain/Apr15/833-791 United Kingdom
Medical Research Council (United Kingdom)MRF-060-0002-RG-HASNA United Kingdom
Sao Paulo Research Fundation2015/00062-1 Brazil
Sao Paulo Research Fundation2016/24686-7 Brazil
National Council for Scientific and Technological Development407438/2013-0 Brazil
CitationJournal: Plos Biol. / Year: 2019
Title: Molecular recognition and maturation of SOD1 by its evolutionarily destabilised cognate chaperone hCCS.
Authors: Sala, F.A. / Wright, G.S.A. / Antonyuk, S.V. / Garratt, R.C. / Hasnain, S.S.
History
DepositionFeb 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
B: Copper chaperone for superoxide dismutase
C: Superoxide dismutase [Cu-Zn]
D: Copper chaperone for superoxide dismutase
E: Superoxide dismutase [Cu-Zn]
F: Copper chaperone for superoxide dismutase
G: Superoxide dismutase [Cu-Zn]
H: Copper chaperone for superoxide dismutase
I: Superoxide dismutase [Cu-Zn]
J: Copper chaperone for superoxide dismutase
K: Superoxide dismutase [Cu-Zn]
L: Copper chaperone for superoxide dismutase
M: Superoxide dismutase [Cu-Zn]
N: Copper chaperone for superoxide dismutase
O: Superoxide dismutase [Cu-Zn]
P: Copper chaperone for superoxide dismutase
Q: Superoxide dismutase [Cu-Zn]
R: Copper chaperone for superoxide dismutase
S: Superoxide dismutase [Cu-Zn]
T: Copper chaperone for superoxide dismutase
U: Superoxide dismutase [Cu-Zn]
V: Copper chaperone for superoxide dismutase
W: Superoxide dismutase [Cu-Zn]
X: Copper chaperone for superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)538,99655
Polymers536,89024
Non-polymers2,10631
Water1,35175
1
A: Superoxide dismutase [Cu-Zn]
B: Copper chaperone for superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1127
Polymers44,7412
Non-polymers3715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Superoxide dismutase [Cu-Zn]
D: Copper chaperone for superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8724
Polymers44,7412
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Superoxide dismutase [Cu-Zn]
F: Copper chaperone for superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8724
Polymers44,7412
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Superoxide dismutase [Cu-Zn]
H: Copper chaperone for superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8724
Polymers44,7412
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Superoxide dismutase [Cu-Zn]
J: Copper chaperone for superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9465
Polymers44,7412
Non-polymers2053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Superoxide dismutase [Cu-Zn]
L: Copper chaperone for superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0206
Polymers44,7412
Non-polymers2794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: Superoxide dismutase [Cu-Zn]
N: Copper chaperone for superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8724
Polymers44,7412
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
O: Superoxide dismutase [Cu-Zn]
P: Copper chaperone for superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8724
Polymers44,7412
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
Q: Superoxide dismutase [Cu-Zn]
R: Copper chaperone for superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9465
Polymers44,7412
Non-polymers2053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
S: Superoxide dismutase [Cu-Zn]
T: Copper chaperone for superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8724
Polymers44,7412
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
U: Superoxide dismutase [Cu-Zn]
V: Copper chaperone for superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8724
Polymers44,7412
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
W: Superoxide dismutase [Cu-Zn]
X: Copper chaperone for superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8724
Polymers44,7412
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.054, 181.054, 141.102
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
51I
61K
71M
81O
91Q
101S
111U
121W
12D
22B
32F
42H
52J
62L
72N
82P
92R
102T
112X
13D
23B
33F
43H
53J
63L
73N
83P
93R
103T
113V
123X

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A2 - 153
2115C2 - 153
3115E2 - 153
4115G2 - 153
5115I2 - 153
6115K2 - 153
7115M2 - 153
8115O2 - 153
9115Q2 - 153
10115S2 - 153
11115U2 - 153
12115W2 - 153
1125D8 - 81
2125B8 - 81
3125F8 - 81
4125H8 - 81
5125J8 - 81
6125L8 - 81
7125N8 - 81
8125P8 - 81
9125R8 - 81
10125T8 - 81
11125X8 - 81
1135D85 - 236
2135B85 - 236
3135F85 - 236
4135H85 - 236
5135J85 - 236
6135L85 - 236
7135N85 - 236
8135P85 - 236
9135R85 - 236
10135T85 - 236
11135V85 - 236
12135X85 - 236

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.874504, -0.153903, -0.459953), (-0.138409, -0.8297, 0.540778), (-0.46485, 0.536575, 0.704274)135.18057, -102.58765, 68.68759
3given(0.210214, 0.977482, 0.018383), (0.977645, -0.21009, -0.008472), (-0.004419, 0.019753, -0.999795)123.06414, -152.21339, -4.06979
4given(-0.999195, -0.039157, 0.008687), (-0.039229, 0.999195, -0.008334), (-0.008354, -0.008668, -0.999928)86.915, 51.80925, 16.52978
5given(-0.334257, -0.822934, 0.459403), (-0.83204, 0.0287, -0.553973), (0.442699, -0.567411, -0.694307)53.72631, 2.26314, -75.38946
6given(-0.724036, -0.68971, 0.008538), (0.689762, -0.723974, 0.009486), (-0.000361, 0.012757, 0.999919)18.83345, -127.56874, 25.17186
7given(0.348096, -0.812645, -0.467372), (0.841831, 0.051602, 0.537269), (-0.412492, -0.580469, 0.702073)-9.61106, -78.88065, -78.18968
8given(-0.620271, 0.784028, -0.023731), (-0.784334, -0.620297, 0.007129), (-0.009131, 0.023035, 0.999693)91.64341, -53.08189, -29.21021
9given(0.669084, -0.595103, -0.445173), (0.732421, 0.42642, 0.530778), (-0.126037, -0.68119, 0.721176)76.60368, -87.03794, -24.28287
10given(-0.898698, -0.43849, 0.008258), (-0.438547, 0.898678, -0.007342), (-0.004202, -0.010219, -0.999939)90.41679, -51.96543, 24.01055
11given(-0.32778, 0.823124, 0.46371), (0.61373, 0.558674, -0.55787), (-0.718259, 0.101734, -0.688298)164.40341, -29.20389, -11.34441
12given(0.847659, 0.254996, 0.465244), (0.499721, -0.678282, -0.538714), (0.178197, 0.689138, -0.702378)53.21856, -58.9887, 15.49172
21given(1), (1), (1)
22given(-0.887212, -0.11841, -0.445909), (-0.164872, -0.82131, 0.546139), (-0.430898, 0.558059, 0.709153)137.53568, -100.12626, 67.90003
23given(-0.300633, -0.851905, 0.428809), (-0.841906, 0.025794, -0.539007), (0.448122, -0.523061, -0.724979)48.25365, 2.88685, -72.42577
24given(0.899855, -0.079348, 0.428912), (0.190621, -0.81291, -0.550309), (0.392333, 0.576958, -0.716376)47.18046, -147.1402, 72.05626
25given(0.219988, 0.975371, -0.016035), (0.975502, -0.21997, 0.002887), (-0.000711, -0.016277, -0.999867)122.35241, -152.85368, -6.96536
26given(0.577797, 0.659612, -0.48069), (-0.449862, 0.748789, 0.486763), (0.68101, -0.065006, 0.729383)119.94861, 17.22084, 10.98672
27given(-0.214304, 0.976124, 0.035426), (-0.976684, -0.214617, 0.005219), (0.012698, -0.033482, 0.999359)190.45428, -74.61199, -27.07075
28given(0.644234, -0.633203, -0.428972), (0.743682, 0.387639, 0.544677), (-0.178605, -0.669918, 0.720631)75.70975, -87.73789, -21.82013
29given(-0.625528, 0.779686, 0.028368), (-0.779899, -0.623857, -0.0506), (-0.021755, -0.053776, 0.998316)90.21838, -51.38205, -27.79763
30given(0.852754, 0.291365, 0.433494), (0.506797, -0.662354, -0.551764), (0.126362, 0.690213, -0.712488)53.0499, -58.99403, 16.82471
31given(-0.880923, -0.471465, -0.041175), (-0.472214, 0.881424, 0.010308), (0.031433, 0.028523, -0.999099)89.70633, -52.19074, 24.36267
41given(1), (1), (1)
42given(-0.883613, -0.139924, -0.446821), (-0.149983, -0.81943, 0.553208), (-0.443546, 0.555837, 0.703073)136.50386, -101.07301, 68.67711
43given(-0.320167, -0.840586, 0.43693), (-0.835665, 0.033328, -0.548228), (0.446271, -0.540652, -0.713119)51.09286, 2.77784, -73.63925
44given(0.891609, -0.102323, 0.441092), (0.176783, -0.818162, -0.547138), (0.41687, 0.565811, -0.711392)44.97826, -147.47388, 70.50285
45given(0.210324, 0.977616, -0.005538), (0.977551, -0.210231, 0.014057), (0.012578, -0.008371, -0.999886)123.01891, -152.19641, -7.28769
46given(0.545034, 0.696875, -0.466158), (-0.45766, 0.713147, 0.531008), (0.702485, -0.076075, 0.707621)125.44721, 15.232, 8.38686
47given(-0.216261, 0.976251, 0.012881), (-0.97631, -0.216332, 0.004419), (0.007101, -0.01162, 0.999907)191.23915, -74.75503, -24.65409
48given(0.656159, -0.613268, -0.439726), (0.736653, 0.394142, 0.54954), (-0.163701, -0.684511, 0.710385)76.46433, -87.69044, -22.01822
49given(-0.617528, 0.786547, -0.001816), (-0.786479, -0.617502, -0.011905), (-0.010485, -0.005924, 0.999927)91.00221, -52.58175, -29.49967
50given(0.853517, 0.268102, 0.4468), (0.497772, -0.673035, -0.547034), (0.154051, 0.689308, -0.707901)53.09093, -58.9287, 16.46659
51given(0.55168, -0.834, 0.009665), (-0.833464, -0.550814, 0.044066), (-0.031427, -0.032365, -0.998982)2.75776, -108.87575, -32.12963
52given(-0.894358, -0.447248, -0.009655), (-0.447165, 0.8944, -0.009583), (0.012922, -0.004253, -0.999907)90.43819, -52.03148, 23.51392

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Components

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Protein , 2 types, 24 molecules ACEGIKMOQSUWBDFHJLNPRTVX

#1: Protein
Superoxide dismutase [Cu-Zn] / Superoxide dismutase 1 / hSod1


Mass: 15763.432 Da / Num. of mol.: 12 / Mutation: C57A; C146A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00441, superoxide dismutase
#2: Protein
Copper chaperone for superoxide dismutase / Superoxide dismutase copper chaperone


Mass: 28977.404 Da / Num. of mol.: 12 / Mutation: C12A; C22A; C25A; C244A; C246A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCS / Production host: Escherichia coli (E. coli) / References: UniProt: O14618

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Non-polymers , 4 types, 106 molecules

#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M PCTP buffer pH 9.0, 20% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.94→49.01 Å / Num. obs: 110021 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 53.95 Å2 / Rmerge(I) obs: 0.165 / Net I/σ(I): 8.5
Reflection shellResolution: 2.94→3.1 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.944 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FOL, 2RSQ

6fol

2rsq


Resolution: 3→49.01 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.912 / SU B: 43.112 / SU ML: 0.34 / Cross valid method: THROUGHOUT / ESU R Free: 0.408 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 5115 4.9 %RANDOM
Rwork0.189 ---
obs0.192 98527 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 73.96 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20.5 Å20 Å2
2--1.01 Å20 Å2
3----3.27 Å2
Refinement stepCycle: LAST / Resolution: 3→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33101 0 60 75 33236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01933644
X-RAY DIFFRACTIONr_bond_other_d0.0010.0231974
X-RAY DIFFRACTIONr_angle_refined_deg1.151.95145469
X-RAY DIFFRACTIONr_angle_other_deg0.854373515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74754496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.10325.1931529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.042155442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.60315195
X-RAY DIFFRACTIONr_chiral_restr0.0660.25072
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0239727
X-RAY DIFFRACTIONr_gen_planes_other0.0020.027464
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_it0.6733.36118076
X-RAY DIFFRACTIONr_mcbond_other0.6733.36118075
X-RAY DIFFRACTIONr_mcangle_it1.2545.03722538
X-RAY DIFFRACTIONr_mcangle_other1.2545.03722539
X-RAY DIFFRACTIONr_scbond_it0.4163.39415568
X-RAY DIFFRACTIONr_scbond_other0.4153.39415568
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8275.07722931
X-RAY DIFFRACTIONr_long_range_B_refined2.56625.41733589
X-RAY DIFFRACTIONr_long_range_B_other2.56625.41833590
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A868medium positional0.160.5
11C868medium positional0.160.5
11E868medium positional0.150.5
11G868medium positional0.20.5
11I868medium positional0.180.5
11K868medium positional0.160.5
11M868medium positional0.170.5
11O868medium positional0.180.5
11Q868medium positional0.310.5
11S868medium positional0.210.5
11U868medium positional0.230.5
11W868medium positional0.160.5
22D376medium positional0.380.5
22B376medium positional0.140.5
22F376medium positional0.250.5
22H376medium positional0.150.5
22J376medium positional0.180.5
22L376medium positional0.190.5
22N376medium positional0.20.5
22P376medium positional0.140.5
22R376medium positional0.160.5
22T376medium positional0.230.5
22X376medium positional0.210.5
33D848medium positional0.110.5
33B848medium positional0.130.5
33F848medium positional0.130.5
33H848medium positional0.110.5
33J848medium positional0.120.5
33L848medium positional0.140.5
33N848medium positional0.120.5
33P848medium positional0.110.5
33R848medium positional0.20.5
33T848medium positional0.140.5
33V848medium positional0.20.5
33X848medium positional0.130.5
11A1190loose positional0.455
11C1190loose positional0.615
11E1190loose positional0.475
11G1190loose positional0.55
11I1190loose positional0.585
11K1190loose positional0.395
11M1190loose positional0.535
11O1190loose positional0.465
11Q1190loose positional0.665
11S1190loose positional0.535
11U1190loose positional0.615
11W1190loose positional0.545
22D511loose positional0.435
22B511loose positional0.35
22F511loose positional0.445
22H511loose positional0.375
22J511loose positional0.355
22L511loose positional0.495
22N511loose positional0.355
22P511loose positional0.345
22R511loose positional0.485
22T511loose positional0.375
22X511loose positional0.415
33D1271loose positional0.335
33B1271loose positional0.515
33F1271loose positional0.455
33H1271loose positional0.435
33J1271loose positional0.355
33L1271loose positional0.525
33N1271loose positional0.435
33P1271loose positional0.445
33R1271loose positional0.375
33T1271loose positional0.55
33V1271loose positional0.595
33X1271loose positional0.415
11A868medium thermal12.652
11C868medium thermal5.032
11E868medium thermal11.582
11G868medium thermal13.932
11I868medium thermal6.262
11K868medium thermal7.822
11M868medium thermal2.922
11O868medium thermal10.132
11Q868medium thermal25.952
11S868medium thermal7.052
11U868medium thermal12.52
11W868medium thermal2.92
22B376medium thermal8.972
22D376medium thermal7.522
22F376medium thermal13.542
22H376medium thermal7.822
22J376medium thermal20.282
22L376medium thermal19.692
22N376medium thermal5.362
22P376medium thermal17.362
22R376medium thermal13.182
22T376medium thermal23.332
22X376medium thermal15.722
33B848medium thermal5.52
33D848medium thermal4.862
33F848medium thermal2.892
33H848medium thermal5.922
33J848medium thermal7.262
33L848medium thermal3.472
33N848medium thermal3.692
33P848medium thermal5.312
33R848medium thermal13.782
33T848medium thermal16.272
33V848medium thermal2.952
33X848medium thermal3.032
11A1190loose thermal12.7310
11C1190loose thermal5.0410
11E1190loose thermal11.610
11G1190loose thermal13.910
11I1190loose thermal6.1210
11K1190loose thermal7.9110
11M1190loose thermal2.7810
11O1190loose thermal10.0610
11Q1190loose thermal26.1710
11S1190loose thermal7.110
11U1190loose thermal12.3910
11W1190loose thermal3.0510
22D511loose thermal8.8210
22B511loose thermal7.410
22F511loose thermal13.4110
22H511loose thermal7.6210
22J511loose thermal20.0710
22L511loose thermal19.8810
22N511loose thermal5.2810
22P511loose thermal17.0210
22R511loose thermal12.9810
22T511loose thermal23.3410
22X511loose thermal15.4210
33D1271loose thermal5.6910
33B1271loose thermal4.9510
33F1271loose thermal2.8510
33H1271loose thermal5.8710
33J1271loose thermal7.5910
33L1271loose thermal3.4910
33N1271loose thermal3.9210
33P1271loose thermal5.4210
33R1271loose thermal14.0210
33T1271loose thermal16.6710
33V1271loose thermal2.9410
33X1271loose thermal3.1710
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 320 -
Rwork0.327 7365 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.9040.05080.18751.27040.93151.71580.02380.04290.06270.0338-0.15820.0003-0.0886-0.18040.13450.4377-0.00720.00660.4798-0.02420.420563.388-31.4749.857
20.8353-0.5825-0.17072.2007-0.08580.918-0.06170.24940.043-0.2210.1248-0.1618-0.1744-0.0883-0.0630.5253-0.04470.09240.4570.0480.400476.445-32.247-13.286
30.7163-0.2433-0.33620.58110.40411.92610.0254-0.13950.01040.32810.05380.07570.06850.0494-0.07910.6674-0.05780.08240.4697-0.00990.251380.294-79.52130.021
40.7203-0.12260.11751.1159-0.82120.87140.05620.1172-0.14370.0794-0.03170.09580.08950.0922-0.02460.5808-0.03420.05740.4057-0.00080.399879.233-93.5497.693
51.1702-0.3392-0.8081.2461-0.04591.671-0.02680.0849-0.0630.1276-0.01150.0130.05590.07590.03820.39340.0611-0.01760.5455-0.0220.3923105.434-83.431-16.021
61.0807-0.46650.03621.54880.24470.41030.1511-0.07210.16670.2771-0.0395-0.09830.06650.2129-0.11150.42870.0082-0.04880.6111-0.0560.3561107.795-70.7467.019
70.61650.3649-0.26830.8964-0.72161.36730.1494-0.05850.0911-0.0808-0.12560.02880.0840.0771-0.02370.5050.01250.07430.453-0.03440.405226.828-82.2417.186
81.63540.6779-0.0592.07190.05380.30670.1359-0.27490.2415-0.0164-0.05620.22260.06820.0865-0.07960.4575-0.10190.0880.4541-0.09220.41313.792-83.19130.262
91.40240.33270.37262.33810.42340.7904-0.25840.2178-0.0507-0.43450.2567-0.1244-0.0305-0.02830.00160.5682-0.16410.0930.6313-0.01870.169462.565-57.294-36.034
101.3127-0.06170.80230.8455-0.13650.5502-0.0791-0.00570.09950.0060.04360.0480.0122-0.02060.03560.419-0.05790.02480.5913-0.00520.342248.389-55.213-13.603
110.6733-0.33620.68271.1849-0.40931.6819-0.16840.2286-0.01420.19360.042-0.0005-0.09070.18210.12630.4414-0.02210.00750.5287-0.06970.376134.017-100.498-14.03
122.1013-1.0392-0.34630.75610.05370.5731-0.00550.2469-0.1746-0.0190.02790.1841-0.11730.1965-0.02230.36220.02090.0160.6214-0.17510.374424.23-109.696-36.628
130.5785-0.44920.41561.9448-0.58572.19220.0361-0.2141-0.0810.1946-0.0240.0289-0.1310.081-0.0120.5045-0.095-0.00980.5925-0.00490.240529.008-107.98553.152
141.06550.59440.4310.741-0.05252.01960.1791-0.14810.0504-0.142-0.321-0.1091-0.06750.3050.14180.3935-0.03570.02560.58240.0620.411142.715-105.44830.93
151.04870.5232-0.79091.142-0.44971.6883-0.0074-0.0110.0043-0.0323-0.00630.03750.0720.01240.01370.5330.06760.03910.41230.04340.3860.215-34.65839.881
160.73390.5207-0.04271.8948-0.26430.98590.17550.31070.2004-0.05730.02410.12920.1508-0.2853-0.19950.47280.0601-0.00730.55740.12510.3449-7.358-24.0216.538
172.2765-0.81510.0770.4220.21531.424-0.637-0.3263-0.06370.27080.33650.0820.03540.09780.30051.01520.41650.05840.57770.05730.06727.5168.4359.954
180.84050.35650.1610.98060.57340.3586-0.09650.14730.18260.28320.0805-0.05210.110.08680.0160.7172-0.0898-0.19320.45440.0850.296638.92515.69437.596
190.6058-0.4040.19291.6211-0.99311.6021-0.10140.1285-0.08040.3542-0.12050.1606-0.32810.24070.22180.644-0.0397-0.03340.38910.03590.317815.34530.40513.803
200.2599-0.3398-0.2941.52390.49181.1952-0.0995-0.1182-0.19510.26340.22630.3462-0.44630.1609-0.12670.89050.15330.2650.27740.11720.32213.5924.13636.851
210.9368-0.51920.19451.5875-0.42442.17180.03830.16140.0597-0.309-0.15620.06420.06230.17090.1180.5520.00830.00780.66640.01890.122416.478-82.27-60.143
220.9657-0.1179-0.04361.53860.13950.4776-0.10790.22890.11640.1404-0.0781-0.01860.0090.12920.18590.4469-0.1069-0.01490.61130.04090.312920.237-74.786-33.675
230.8810.3074-0.65031.3782-0.32732.5172-0.03930.18720.0844-0.18920.1035-0.01450.0885-0.0887-0.06420.54350.05510.02910.53870.08520.243421.358-19.948-6.111
240.5943-0.4023-0.63781.15560.42940.8659-0.0142-0.1617-0.2125-0.088-0.1178-0.015-0.0313-0.05820.13190.47120.09830.06550.48950.09640.422628.249-32.0316.491
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 155
2X-RAY DIFFRACTION2B9 - 400
3X-RAY DIFFRACTION3C1 - 155
4X-RAY DIFFRACTION4D8 - 400
5X-RAY DIFFRACTION5E1 - 155
6X-RAY DIFFRACTION6F9 - 400
7X-RAY DIFFRACTION7G1 - 155
8X-RAY DIFFRACTION8H9 - 400
9X-RAY DIFFRACTION9I1 - 155
10X-RAY DIFFRACTION10J9 - 400
11X-RAY DIFFRACTION11K1 - 155
12X-RAY DIFFRACTION12L9 - 400
13X-RAY DIFFRACTION13M1 - 155
14X-RAY DIFFRACTION14N9 - 400
15X-RAY DIFFRACTION15O1 - 155
16X-RAY DIFFRACTION16P8 - 400
17X-RAY DIFFRACTION17Q1 - 155
18X-RAY DIFFRACTION18R9 - 400
19X-RAY DIFFRACTION19S1 - 155
20X-RAY DIFFRACTION20T9 - 400
21X-RAY DIFFRACTION21U1 - 155
22X-RAY DIFFRACTION22V85 - 400
23X-RAY DIFFRACTION23W1 - 155
24X-RAY DIFFRACTION24X9 - 400

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