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- PDB-4v4f: The structure of the trp RNA-binding attenuation protein (TRAP) b... -

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Basic information

Entry
Database: PDB / ID: 4v4f
TitleThe structure of the trp RNA-binding attenuation protein (TRAP) bound to a RNA molecule containing UAGAU repeats
Components
  • 5'-R(*UP*AP*GP*AP*UP)-3'
  • TRANSCRIPTION ATTENUATION PROTEIN MTRB
KeywordsRNA BINDING PROTEIN / TRANSCRIPTION ATTENUATION / RNA-BINDING PROTEIN / TRP RNA
Function / homology
Function and homology information


DNA-templated transcription termination / regulation of DNA-templated transcription / RNA binding / identical protein binding
Similarity search - Function
Transcription attenuation protein MtrB / Tryptophan RNA-binding attenuator protein domain / Tryptophan RNA-binding attenuator protein / Tryptophan RNA-binding attenuator protein-like domain superfamily
Similarity search - Domain/homology
TRYPTOPHAN / RNA / Transcription attenuation protein MtrB
Similarity search - Component
Biological speciesBACILLUS STEAROTHERMOPHILUS (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHopcroft, N.H. / Manfredo, A. / Wendt, A.L. / Brzozowski, A.M. / Gollnick, P. / Antson, A.A.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: The Interaction of RNA with Trap: The Role of Triplet Repeats and Separating Spacer Nucleotides
Authors: Hopcroft, N.H. / Manfredo, A. / Wendt, A.L. / Brzozowski, A.M. / Gollnick, P. / Antson, A.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Specificity of Trap/RNA Interactions: Crystal Structures of Complexes with Two Different RNA Sequences
Authors: Hopcroft, N.H. / Wendt, A.L. / Gollnick, P. / Antson, A.A.
#2: Journal: Nature / Year: 1999
Title: Structure of the Trp RNA-Binding Attenuation Protein, Trap, Bound to RNA
Authors: Antson, A.A. / Dodson, E.J. / Dodson, G.G. / Greaves, R.B. / Chen, X.-P. / Gollnick, P.
History
DepositionDec 8, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 1UTF, 1UTV
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Jul 29, 2020Group: Advisory / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A0: 5'-R(*UP*AP*GP*AP*UP)-3'
A1: 5'-R(*UP*AP*GP*AP*UP)-3'
A2: 5'-R(*UP*AP*GP*AP*UP)-3'
A3: 5'-R(*UP*AP*GP*AP*UP)-3'
A4: 5'-R(*UP*AP*GP*AP*UP)-3'
A5: 5'-R(*UP*AP*GP*AP*UP)-3'
A6: 5'-R(*UP*AP*GP*AP*UP)-3'
A7: 5'-R(*UP*AP*GP*AP*UP)-3'
A8: 5'-R(*UP*AP*GP*AP*UP)-3'
A9: 5'-R(*UP*AP*GP*AP*UP)-3'
AA: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AB: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AC: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AD: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AE: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AF: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AG: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AH: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AI: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AJ: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AK: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AL: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AM: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AN: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AO: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AP: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AQ: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AR: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AS: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AT: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AU: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AV: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AZ: 5'-R(*UP*AP*GP*AP*UP)-3'
B0: 5'-R(*UP*AP*GP*AP*UP)-3'
B1: 5'-R(*UP*AP*GP*AP*UP)-3'
B2: 5'-R(*UP*AP*GP*AP*UP)-3'
B3: 5'-R(*UP*AP*GP*AP*UP)-3'
B4: 5'-R(*UP*AP*GP*AP*UP)-3'
B5: 5'-R(*UP*AP*GP*AP*UP)-3'
B6: 5'-R(*UP*AP*GP*AP*UP)-3'
B7: 5'-R(*UP*AP*GP*AP*UP)-3'
B8: 5'-R(*UP*AP*GP*AP*UP)-3'
B9: 5'-R(*UP*AP*GP*AP*UP)-3'
BA: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BB: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BC: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BD: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BE: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BF: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BG: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BH: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BI: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BJ: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BK: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BL: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BM: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BN: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BO: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BP: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BQ: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BR: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BS: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BT: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BU: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BV: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BZ: 5'-R(*UP*AP*GP*AP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,872110
Polymers397,88666
Non-polymers8,98644
Water59,7743318
1
A0: 5'-R(*UP*AP*GP*AP*UP)-3'
A1: 5'-R(*UP*AP*GP*AP*UP)-3'
A2: 5'-R(*UP*AP*GP*AP*UP)-3'
A3: 5'-R(*UP*AP*GP*AP*UP)-3'
A4: 5'-R(*UP*AP*GP*AP*UP)-3'
A5: 5'-R(*UP*AP*GP*AP*UP)-3'
A6: 5'-R(*UP*AP*GP*AP*UP)-3'
A7: 5'-R(*UP*AP*GP*AP*UP)-3'
A8: 5'-R(*UP*AP*GP*AP*UP)-3'
A9: 5'-R(*UP*AP*GP*AP*UP)-3'
AA: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AB: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AC: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AD: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AE: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AF: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AG: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AH: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AI: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AJ: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AK: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AZ: 5'-R(*UP*AP*GP*AP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,35933
Polymers108,11222
Non-polymers2,24611
Water39622
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26530 Å2
ΔGint-78.5 kcal/mol
Surface area27020 Å2
MethodPISA
2
AL: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AM: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AN: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AO: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AP: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AQ: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AR: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AS: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AT: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AU: TRANSCRIPTION ATTENUATION PROTEIN MTRB
AV: TRANSCRIPTION ATTENUATION PROTEIN MTRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,07822
Polymers90,83111
Non-polymers2,24611
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26670 Å2
ΔGint-75.7 kcal/mol
Surface area27680 Å2
MethodPISA
3
B0: 5'-R(*UP*AP*GP*AP*UP)-3'
B1: 5'-R(*UP*AP*GP*AP*UP)-3'
B2: 5'-R(*UP*AP*GP*AP*UP)-3'
B3: 5'-R(*UP*AP*GP*AP*UP)-3'
B4: 5'-R(*UP*AP*GP*AP*UP)-3'
B5: 5'-R(*UP*AP*GP*AP*UP)-3'
B6: 5'-R(*UP*AP*GP*AP*UP)-3'
B7: 5'-R(*UP*AP*GP*AP*UP)-3'
B8: 5'-R(*UP*AP*GP*AP*UP)-3'
B9: 5'-R(*UP*AP*GP*AP*UP)-3'
BA: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BB: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BC: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BD: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BE: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BF: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BG: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BH: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BI: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BJ: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BK: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BZ: 5'-R(*UP*AP*GP*AP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,35933
Polymers108,11222
Non-polymers2,24611
Water39622
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
BL: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BM: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BN: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BO: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BP: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BQ: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BR: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BS: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BT: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BU: TRANSCRIPTION ATTENUATION PROTEIN MTRB
BV: TRANSCRIPTION ATTENUATION PROTEIN MTRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,07822
Polymers90,83111
Non-polymers2,24611
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)113.907, 133.986, 232.826
Angle α, β, γ (deg.)90.00, 100.11, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AA
21AB
31AC
41AD
51AE
61AF
71AG
81AH
91AI
101AJ
111AK
121BA
131BB
141BC
151BD
161BE
171BF
181BG
191BH
201BI
211BJ
221BK
12A1
22A2
32A3
42A4
52A5
62A7
72A8
82AZ
92B0
102B1
112B3
122B4
132B5
142B6
152B7
162B8
172B9
182BZ
13A0
23A6
33A9
43B2
14A0
24A1
34A2
44A3
54A4
64A5
74A6
84A7
94A8
104A9
114AZ
124B0
134B1
144B2
154B3
164B4
174B5
184B6
194B7
204B8
214B9
224BZ
15AL
25AM
35AN
45AO
55AP
65AQ
75AR
85AS
95AT
105AU
115AV
125BL
135BM
145BN
155BO
165BP
175BQ
185BR
195BS
205BT
215BU
225BV

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113AA8 - 72
2113AB8 - 72
3113AC8 - 72
4113AD8 - 72
5113AE8 - 72
6113AF8 - 72
7113AG8 - 72
8113AH8 - 72
9113AI8 - 72
10113AJ8 - 72
11113AK8 - 72
12113BA8 - 72
13113BB8 - 72
14113BC8 - 72
15113BD8 - 72
16113BE8 - 72
17113BF8 - 72
18113BG8 - 72
19113BH8 - 72
20113BI8 - 72
21113BJ8 - 72
22113BK8 - 72
1211AB101
2211AC101
3211AD101
4211AE101
5211AF101
6211AG101
7211AH101
8211AI101
9211AJ101
10211AK101
11211AA101
12211BB101
13211BC101
14211BD101
15211BE101
16211BF101
17211BG101
18211BH101 - 81
19211BI101 - 81
20211BJ101 - 81
21211BK101 - 81
22211BA101 - 81
1124A1102
2124A2102
3124A3102
4124A4102
5124A5102
6124A7102
7124A8102
8124AZ102
9124B0102
10124B1102
11124B3102
12124B4102
13124B5102
14124B6102
15124B7102
16124B8102
17124B9102
18124BZ102
1134A0102
2134A6102
3134A9102
4134B2102
1144A0103 - 105
2144A1103 - 105
3144A2103 - 105
4144A3103 - 105
5144A4103 - 105
6144A5103 - 105
7144A6103 - 105
8144A7103 - 105
9144A8103 - 105
10144A9103 - 105
11144AZ103 - 105
12144B0103 - 105
13144B1103 - 105
14144B2103 - 105
15144B3103 - 105
16144B4103 - 105
17144B5103 - 105
18144B6103 - 105
19144B7103 - 105
20144B8103 - 105
21144B9103 - 105
22144BZ103 - 105
1153AL208 - 272
2153AM208 - 272
3153AN208 - 272
4153AO208 - 272
5153AP208 - 272
6153AQ208 - 272
7153AR208 - 272
8153AS208 - 272
9153AT208 - 272
10153AU208 - 272
11153AV208 - 272
12153BL8 - 72
13153BM8 - 72
14153BN8 - 72
15153BO8 - 72
16153BP8 - 72
17153BQ8 - 72
18153BR8 - 72
19153BS8 - 72
20153BT8 - 72
21153BU8 - 72
22153BV8 - 72
1251AM301
2251AN301
3251AO301
4251AP301
5251AQ301
6251AR301
7251AS301
8251AT301
9251AU301
10251AV301
11251AL301
12251BM101
13251BN101
14251BO101
15251BP101
16251BQ101
17251BR101
18251BS101
19251BT101
20251BU101
21251BV101
22251BL101

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: RNA chain ...
5'-R(*UP*AP*GP*AP*UP)-3'


Mass: 1570.992 Da / Num. of mol.: 22 / Source method: obtained synthetically / Details: SYNTHETIC RNA IN-VITRO TRANSCRIPTION / Source: (synth.) synthetic construct
#2: Protein ...
TRANSCRIPTION ATTENUATION PROTEIN MTRB / TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN / TRP RNA-BINDING ATTENUATION PROTEIN / TRAP


Mass: 8257.377 Da / Num. of mol.: 44
Source method: isolated from a genetically manipulated source
Details: TWO PROTEIN 11MERS (CHAINS A-K AND L-V) / Source: (gene. exp.) BACILLUS STEAROTHERMOPHILUS (bacteria) / Plasmid: PTZSTMTRB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SG62052/PGP1-2 / References: UniProt: Q9X6J6
#3: Chemical...
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3318 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREQUIRED FOR TRANSCRIPTION REGULATION IN THE TRP OPERON. THIS TRANS-ACTING FACTOR SEEMS TO ...REQUIRED FOR TRANSCRIPTION REGULATION IN THE TRP OPERON. THIS TRANS-ACTING FACTOR SEEMS TO RECOGNIZE A 10 BASES NUCLEOTIDE SEQUENCE IN THE TRP LEADER TRANSCRIPT CAUSING TRANSCRIPTION TERMINATION.
Sequence detailsRNA MOLECULE CONTAINS 11 UAG TRIPLETS SEPARATED BY AU DINUCLEOTIDES, RNA IS PRESENT IN RESIDUES 101- ...RNA MOLECULE CONTAINS 11 UAG TRIPLETS SEPARATED BY AU DINUCLEOTIDES, RNA IS PRESENT IN RESIDUES 101-105 IN CHAINS A-K OF THE STRUCTURE

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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: 4.4 Å3/Da / Density % sol: 72.02 %
Crystal growpH: 8
Details: 0.2M K-GLUTAMATE, 50 MM TRIETHANOLAMINE PH8.0, 10MM MGCL2, 8-11% MONOMETHYL ETHER PEG 2000, +0.4M KCL AT END, pH 8.00

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9336
DetectorDate: Jun 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9336 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. obs: 251906 / % possible obs: 92.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 19.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 2.7 / % possible all: 58

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Processing

Software
NameVersionClassification
AMoREmodel building
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C9S
Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.03 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1248 0.5 %RANDOM
Rwork0.186 ---
obs0.186 249451 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.53 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å20 Å22.02 Å2
2---1.32 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11960 584 330 1682 14556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02126139
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.97635342
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16453044
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1060.24032
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219017
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.210117
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.22770
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.260
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.206215306
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.148424515
X-RAY DIFFRACTIONr_scbond_it5.1661010833
X-RAY DIFFRACTIONr_scangle_it6.5881510827
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
11AA275tight positional0.070.1
12AB275tight positional0.060.1
13AC275tight positional0.070.1
14AD275tight positional0.060.1
15AE275tight positional0.070.1
16AF275tight positional0.070.1
17AG275tight positional0.080.1
18AH275tight positional0.070.1
19AI275tight positional0.080.1
110AJ275tight positional0.060.1
111AK275tight positional0.060.1
112AL275tight positional0.090.1
113AM275tight positional0.070.1
114AN275tight positional0.070.1
115AO275tight positional0.060.1
116AP275tight positional0.070.1
117AQ275tight positional0.070.1
118AR275tight positional0.070.1
119AS275tight positional0.070.1
120AT275tight positional0.070.1
121AU275tight positional0.060.1
122AV275tight positional0.060.1
51AA273tight positional0.070.1
52AB273tight positional0.060.1
53AC273tight positional0.070.1
54AD273tight positional0.080.1
55AE273tight positional0.090.1
56AF273tight positional0.080.1
57AG273tight positional0.080.1
58AH273tight positional0.080.1
59AI273tight positional0.090.1
510AJ273tight positional0.080.1
511AK273tight positional0.070.1
512AL273tight positional0.070.1
513AM273tight positional0.070.1
514AN273tight positional0.080.1
515AO273tight positional0.070.1
516AP273tight positional0.080.1
517AQ273tight positional0.080.1
518AR273tight positional0.10.1
519AS273tight positional0.070.1
520AT273tight positional0.070.1
521AU273tight positional0.070.1
522AV273tight positional0.090.1
21AB22medium positional0.150.2
22AC22medium positional0.110.2
23AD22medium positional0.250.2
24AE22medium positional0.140.2
25AF22medium positional0.20.2
26AH22medium positional0.20.2
27AI22medium positional0.090.2
28AK22medium positional0.080.2
29AL22medium positional0.180.2
210AM22medium positional0.210.2
211AO22medium positional0.20.2
212AP22medium positional0.180.2
213AQ22medium positional0.10.2
214AR22medium positional0.150.2
215AS22medium positional0.110.2
216AT22medium positional0.140.2
217AU22medium positional0.150.2
218AV22medium positional0.120.2
31AA18medium positional0.080.2
32AG18medium positional0.060.2
33AJ18medium positional0.120.2
34AN18medium positional0.050.2
41AA23medium positional0.080.2
42AB23medium positional0.090.2
43AC23medium positional0.050.2
44AD23medium positional0.050.2
45AE23medium positional0.050.2
46AF23medium positional0.070.2
47AG23medium positional0.10.2
48AH23medium positional0.090.2
49AI23medium positional0.120.2
410AJ23medium positional0.10.2
411AK23medium positional0.060.2
412AL23medium positional0.080.2
413AM23medium positional0.110.2
414AN23medium positional0.10.2
415AO23medium positional0.090.2
416AP23medium positional0.120.2
417AQ23medium positional0.060.2
418AR23medium positional0.10.2
419AS23medium positional0.090.2
420AT23medium positional0.070.2
421AU23medium positional0.080.2
422AV23medium positional0.060.2
11AA244loose positional0.312
12AB244loose positional0.312
13AC244loose positional0.292
14AD244loose positional0.32
15AE244loose positional0.322
16AF244loose positional0.372
17AG244loose positional0.262
18AH244loose positional0.422
19AI244loose positional0.472
110AJ244loose positional0.242
111AK244loose positional0.242
112AL244loose positional0.362
113AM244loose positional0.262
114AN244loose positional0.242
115AO244loose positional0.322
116AP244loose positional0.312
117AQ244loose positional0.262
118AR244loose positional0.242
119AS244loose positional0.362
120AT244loose positional0.342
121AU244loose positional0.222
122AV244loose positional0.262
51AA244loose positional0.482
52AB244loose positional0.432
53AC244loose positional0.52
54AD244loose positional0.612
55AE244loose positional1.012
56AF244loose positional0.462
57AG244loose positional0.572
58AH244loose positional0.522
59AI244loose positional0.792
510AJ244loose positional0.592
511AK244loose positional0.512
512AL244loose positional0.642
513AM244loose positional0.552
514AN244loose positional0.52
515AO244loose positional0.52
516AP244loose positional0.542
517AQ244loose positional0.552
518AR244loose positional0.812
519AS244loose positional0.562
520AT244loose positional0.492
521AU244loose positional0.492
522AV244loose positional0.872
11AA275tight thermal1.372
12AB275tight thermal1.192
13AC275tight thermal1.022
14AD275tight thermal1.062
15AE275tight thermal1.122
16AF275tight thermal1.012
17AG275tight thermal1.182
18AH275tight thermal1.122
19AI275tight thermal12
110AJ275tight thermal1.042
111AK275tight thermal0.982
112AL275tight thermal1.12
113AM275tight thermal1.172
114AN275tight thermal12
115AO275tight thermal1.042
116AP275tight thermal1.112
117AQ275tight thermal0.972
118AR275tight thermal1.352
119AS275tight thermal1.032
120AT275tight thermal12
121AU275tight thermal1.032
122AV275tight thermal1.12
51AA273tight thermal0.862
52AB273tight thermal0.92
53AC273tight thermal12
54AD273tight thermal0.932
55AE273tight thermal0.942
56AF273tight thermal1.012
57AG273tight thermal1.22
58AH273tight thermal1.042
59AI273tight thermal1.052
510AJ273tight thermal0.982
511AK273tight thermal0.912
512AL273tight thermal0.962
513AM273tight thermal1.072
514AN273tight thermal1.322
515AO273tight thermal0.952
516AP273tight thermal12
517AQ273tight thermal0.892
518AR273tight thermal0.992
519AS273tight thermal1.012
520AT273tight thermal1.242
521AU273tight thermal0.962
522AV273tight thermal1.062
21AB22medium thermal3.125
22AC22medium thermal1.785
23AD22medium thermal2.645
24AE22medium thermal35
25AF22medium thermal3.025
26AH22medium thermal4.045
27AI22medium thermal3.85
28AK22medium thermal3.085
29AL22medium thermal4.685
210AM22medium thermal2.565
211AO22medium thermal2.985
212AP22medium thermal2.975
213AQ22medium thermal2.045
214AR22medium thermal5.055
215AS22medium thermal2.675
216AT22medium thermal3.635
217AU22medium thermal3.525
218AV22medium thermal3.375
31AA18medium thermal2.575
32AG18medium thermal2.935
33AJ18medium thermal4.75
34AN18medium thermal3.555
41AA23medium thermal3.075
42AB23medium thermal2.945
43AC23medium thermal3.15
44AD23medium thermal3.825
45AE23medium thermal2.585
46AF23medium thermal3.875
47AG23medium thermal3.415
48AH23medium thermal3.325
49AI23medium thermal4.585
410AJ23medium thermal2.95
411AK23medium thermal2.265
412AL23medium thermal5.655
413AM23medium thermal4.395
414AN23medium thermal5.35
415AO23medium thermal2.375
416AP23medium thermal4.215
417AQ23medium thermal3.875
418AR23medium thermal5.455
419AS23medium thermal2.115
420AT23medium thermal2.755
421AU23medium thermal2.985
422AV23medium thermal2.755
11AA244loose thermal3.5210
12AB244loose thermal2.9710
13AC244loose thermal3.0510
14AD244loose thermal2.9110
15AE244loose thermal2.8910
16AF244loose thermal3.3110
17AG244loose thermal3.0610
18AH244loose thermal3.1410
19AI244loose thermal3.2810
110AJ244loose thermal2.9510
111AK244loose thermal3.1510
112AL244loose thermal3.4510
113AM244loose thermal2.8910
114AN244loose thermal2.7510
115AO244loose thermal2.9510
116AP244loose thermal2.7310
117AQ244loose thermal2.8110
118AR244loose thermal3.4210
119AS244loose thermal3.1310
120AT244loose thermal3.5310
121AU244loose thermal3.1310
122AV244loose thermal2.8510
51AA244loose thermal3.1310
52AB244loose thermal2.9210
53AC244loose thermal2.8210
54AD244loose thermal2.9110
55AE244loose thermal3.710
56AF244loose thermal3.1710
57AG244loose thermal3.2910
58AH244loose thermal3.4610
59AI244loose thermal3.9810
510AJ244loose thermal3.5410
511AK244loose thermal2.9110
512AL244loose thermal3.3310
513AM244loose thermal3.3810
514AN244loose thermal3.5310
515AO244loose thermal3.1310
516AP244loose thermal2.9910
517AQ244loose thermal3.3610
518AR244loose thermal3.110
519AS244loose thermal3.3510
520AT244loose thermal3.3110
521AU244loose thermal3.2910
522AV244loose thermal3.4610
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.224 60
Rwork0.181 12084
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.8778-0.5497-0.88911.4036-1.68576.8965-0.080.096-0.11750.00940.17030.23480.2875-0.5141-0.09030.0604-0.053-0.09880.30630.0080.1855-9.9983-14.988662.6831
22.9422-0.0373-1.89583.5099-1.99546.0924-0.06490.14080.03240.21180.17720.34070.0904-0.425-0.11230.13680.01940.00540.23270.02360.2452-26.7116-6.158191.4535
31.0517-0.2562-1.77322.8267-1.69264.8938-0.10270.1999-0.0161-0.03110.10810.30990.2198-0.435-0.00540.0718-0.0044-0.08750.35360.04450.2076-13.9354-0.157560.7243
42.74830.5676-2.20284.646-2.16795.01220.03020.19530.10330.22790.11920.4869-0.0414-0.3652-0.14940.16720.06790.02520.2310.03150.2741-25.85568.740391.7773
51.97230.8947-2.30972.5937-0.57883.70480.0480.29980.24680.09530.10410.2746-0.1429-0.5028-0.15210.10790.0734-0.04810.32060.07610.2133-9.845314.865263.0276
62.96630.6808-2.12753.6046-0.55124.11520.06440.07480.15860.2271-0.02550.2448-0.0906-0.2618-0.03890.24260.05870.03850.18690.00410.2656-17.544520.858295.869
73.40281.2812-2.49182.3212-0.05414.34270.20760.18580.32980.11930.01140.2476-0.3403-0.4223-0.2190.20440.0782-0.0080.19560.04390.2040.365924.967367.996
84.78031.7305-2.31562.3966-0.29683.58280.0417-0.08780.17280.1492-0.04680.1304-0.1527-0.09630.00510.31380.0436-0.00540.1244-0.02150.1994-4.94426.2285101.7068
94.31160.7718-1.68451.4433-0.34134.17040.2202-0.21780.33820.0895-0.09290.0105-0.4828-0.0679-0.12730.1994-0.0013-0.05260.1754-0.01650.196514.722127.269774.9998
102.9394-0.7822-0.83641.65861.34632.793-0.04760.02290.09620.2260.0369-0.0119-0.0901-0.06810.01060.3245-0.0058-0.05980.1099-0.00420.19778.400122.9047108.2189
113.9833-0.7954-1.49311.44190.35524.53240.1087-0.12690.20570.13790.0587-0.2004-0.4870.097-0.16740.1879-0.0309-0.11010.21480.00650.224527.393920.882980.8427
123.109-1.3001-1.85042.20131.08213.93660.0423-0.10880.04980.32310.0694-0.1197-0.18720.1514-0.11160.3208-0.0243-0.15380.11870.00460.195117.995712.2326112.6934
133.197-1.3493-2.17751.71010.4544.72950.0696-0.24830.10790.24650.0682-0.1227-0.2140.4237-0.13780.1631-0.0183-0.13590.25920.00990.254934.94037.095384.1897
141.7119-1.3666-1.2132.69720.8974.4315-0.0237-0.0976-0.00960.55350.0727-0.0634-0.07870.2547-0.0490.3402-0.0335-0.17510.14520.00970.203120.8302-2.4209114.0383
151.7067-0.3112-1.58692.54170.82754.34330.0164-0.2141-0.01380.28910.0588-0.2092-0.02820.4979-0.07520.13090.0321-0.14050.27610.04460.271834.9751-8.407784.1558
161.697-0.6749-1.72694.05390.75015.4785-0.0422-0.1004-0.01490.41640.0049-0.1440.19490.21290.03730.2709-0.0308-0.16230.12040.0170.188816.0951-16.4905111.7637
170.96280.4801-0.71572.1851.33885.6362-0.0318-0.0907-0.08420.2896-0.0083-0.11790.3390.42720.04010.17790.0682-0.08210.21050.04090.209327.2176-21.40180.4409
181.3890.83310.54172.65350.06254.68280.0334-0.0407-0.03950.2835-0.0633-0.09130.1663-0.01810.02990.2806-0.0068-0.05730.10290.00740.16085.1954-25.473106.5229
192.3760.9575-0.60050.90681.05376.0275-0.0394-0.1741-0.21380.1342-0.098-0.13070.55430.08480.13740.25290.022-0.02670.14790.01820.186814.4078-27.618374.2632
202.11470.626-0.4331.2548-0.9046.4944-0.0567-0.0133-0.08360.0518-0.04920.02080.2506-0.10.10590.2216-0.0113-0.00730.12110.0110.1547-8.2105-26.4222100.0907
212.9318-0.4993-0.47951.4616-0.49616.6743-0.1317-0.0292-0.29420.0020.07350.10580.5435-0.31540.05820.1733-0.0707-0.04290.2017-0.00540.16550.6006-25.462767.5164
223.0636-0.3953-0.71931.7476-1.58296.4213-0.11890.0796-0.13080.09940.12810.1370.1568-0.4168-0.00920.1474-0.0314-0.00870.20080.00720.1874-20.1187-19.277794.4992
234.14690.7631-1.94960.6737-0.384.53640.1280.21510.3567-0.04180.05610.0899-0.456-0.1375-0.1840.14720.0527-0.0520.23390.04920.196111.044322.854335.0021
241.7557-0.296-0.04330.8953-0.17246.7893-0.04150.108-0.1578-0.0121-0.0013-0.14140.38550.19430.04280.14930.0415-0.00450.173-0.01950.289243.1151-26.066813.1135
252.39361.3826-1.77442.3494-0.27334.19520.02670.20270.1691-0.21230.17280.1561-0.2335-0.3757-0.19950.08890.0325-0.09170.34350.05210.17472.44219.837730.8761
263.3087-0.4047-0.14031.28371.99037.1187-0.07990.1035-0.16550.03650.1589-0.16860.35410.3165-0.0790.08440.0646-0.02710.24510.00270.332955.4563-20.216819.1483
271.0240.7491-1.14223.2062-0.64044.08890.02320.13750.0561-0.37960.07870.12290.0831-0.4084-0.10190.1371-0.0307-0.0770.31030.01790.18081.6477-5.894130.3019
282.1105-0.2293-0.90152.52792.22194.4776-0.0734-0.01170.095-0.08370.1-0.33120.10470.2567-0.02660.03590.0226-0.05340.3040.02370.361262.9843-7.478122.7158
291.1886-0.0494-1.52013.0204-1.2385.486-0.03180.1852-0.1046-0.28910.06780.05830.3392-0.48-0.03610.1592-0.0383-0.05120.277-0.0120.17298.0569-19.53733.3395
303.05140.0043-1.55753.15251.31044.0269-0.0513-0.0779-0.0352-0.18250.0448-0.3991-0.06290.31630.00650.07620.0034-0.00480.29650.03860.372763.14017.561223.0188
312.5729-0.902-0.98631.2426-1.31656.1192-0.0660.1688-0.2068-0.1943-0.08240.00690.5574-0.10730.14840.24480.0026-0.00730.1674-0.01490.179920.6208-26.968939.0651
322.8429-1.0355-3.43513.57450.44555.33070.179-0.19040.1052-0.1425-0.1166-0.3037-0.27820.3457-0.06240.0841-0.0297-0.02710.26150.02790.331655.824920.237619.8265
332.3545-0.2011-0.52491.67350.47456.5946-0.05550.0754-0.2472-0.0258-0.0393-0.14140.45680.20490.09480.13810.0606-0.02740.21260.03120.236734.5831-25.95145.6769
344.7388-0.2563-2.97412.1439-1.08424.52240.21120.02850.2134-0.0067-0.041-0.1343-0.29180.0976-0.17010.1346-0.00660.0070.16970.01430.269743.640426.745414.1175
352.21450.2653-1.04791.51011.01455.4546-0.1492-0.129-0.1594-0.03820.1245-0.27810.31890.27980.02470.08830.0626-0.06710.29360.0530.290645.7435-17.276751.0259
363.59070.5463-0.90341.9731-1.00293.20190.04530.0860.0973-0.05240.0886-0.0785-0.2193-0.045-0.13390.15870.01810.01150.19480.04170.195930.152224.82137.614
370.90090.1518-1.14413.00191.39134.5829-0.0442-0.2765-0.0643-0.11240.1057-0.41280.1390.3801-0.06150.0765-0.0005-0.07190.35070.02710.315150.7397-2.153953.6495
383.32941.1697-1.72351.8029-1.37384.05510.05540.16750.0408-0.21490.0449-0.0352-0.0963-0.2037-0.10030.14550.0172-0.06770.24630.03690.157119.917715.08732.5927
392.4116-0.9208-2.40273.09120.98894.18330.0256-0.3650.0574-0.1012-0.0169-0.4321-0.07440.5234-0.00870.094-0.0251-0.09010.31310.01930.298847.746113.001152.385
402.61831.4834-1.23743.3992-0.73254.2919-0.09620.0736-0.0141-0.50010.0509-0.083-0.0025-0.16640.04530.1684-0.0039-0.07580.25560.01670.15816.09190.7710.5663
413.2155-1.4281-2.47552.15830.08883.88950.1831-0.14090.23640.0216-0.0681-0.2825-0.23530.3487-0.11510.1431-0.0333-0.06130.2116-0.0230.253737.810324.120747.8105
421.39990.156-1.11933.2593-0.88725.6359-0.03970.1346-0.0453-0.45310.0208-0.04540.1243-0.30140.01890.1507-0.0098-0.07930.2720.00010.180819.6001-13.77782.1153
434.3886-0.942-2.05260.6968-0.16084.18850.29160.110.36770.073-0.063-0.1079-0.44690.0929-0.22860.18690.0028-0.01550.17420.00290.225224.098627.524341.2992
441.4797-0.8868-0.53213.3402-0.70854.3023-0.01620.1486-0.0083-0.089-0.0198-0.04640.186-0.09570.0360.1601-0.0287-0.02570.2139-0.04390.168329.7133-23.81056.8411
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1AA1 - 199
2X-RAY DIFFRACTION2AL201 - 299
3X-RAY DIFFRACTION3AB1 - 199
4X-RAY DIFFRACTION4AM201 - 299
5X-RAY DIFFRACTION5AC1 - 199
6X-RAY DIFFRACTION6AN201 - 299
7X-RAY DIFFRACTION7AD1 - 199
8X-RAY DIFFRACTION8AO201 - 299
9X-RAY DIFFRACTION9AE1 - 199
10X-RAY DIFFRACTION10AP201 - 299
11X-RAY DIFFRACTION11AF1 - 199
12X-RAY DIFFRACTION12AQ201 - 299
13X-RAY DIFFRACTION13AG1 - 199
14X-RAY DIFFRACTION14AR201 - 299
15X-RAY DIFFRACTION15AH1 - 199
16X-RAY DIFFRACTION16AS201 - 299
17X-RAY DIFFRACTION17AI1 - 199
18X-RAY DIFFRACTION18AT201 - 299
19X-RAY DIFFRACTION19AJ1 - 199
20X-RAY DIFFRACTION20AU201 - 299
21X-RAY DIFFRACTION21AK1 - 199
22X-RAY DIFFRACTION22AS201 - 299
23X-RAY DIFFRACTION23BA1 - 199
24X-RAY DIFFRACTION24BL201 - 299
25X-RAY DIFFRACTION25BB1 - 199
26X-RAY DIFFRACTION26BM201 - 299
27X-RAY DIFFRACTION27BC1 - 199
28X-RAY DIFFRACTION28BN201 - 299
29X-RAY DIFFRACTION29BD1 - 199
30X-RAY DIFFRACTION30BO201 - 299
31X-RAY DIFFRACTION31BE1 - 199
32X-RAY DIFFRACTION32BP201 - 299
33X-RAY DIFFRACTION33BF1 - 199
34X-RAY DIFFRACTION34BQ201 - 299
35X-RAY DIFFRACTION35BG1 - 199
36X-RAY DIFFRACTION36BR201 - 299
37X-RAY DIFFRACTION37BH1 - 199
38X-RAY DIFFRACTION38BS201 - 299
39X-RAY DIFFRACTION39BI1 - 199
40X-RAY DIFFRACTION40BT201 - 299
41X-RAY DIFFRACTION41BJ1 - 199
42X-RAY DIFFRACTION42BU201 - 299
43X-RAY DIFFRACTION43BB1 - 199
44X-RAY DIFFRACTION44BV201 - 299

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