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- PDB-3h0l: Structure of trna-dependent amidotransferase gatcab from aquifex ... -

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Basic information

Entry
Database: PDB / ID: 3h0l
TitleStructure of trna-dependent amidotransferase gatcab from aquifex aeolicus
Components
  • (Glutamyl-tRNA(Gln) amidotransferase subunit ...) x 2
  • Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
KeywordsLIGASE / MULTI PROTEIN COMPLEX / Protein biosynthesis
Function / homology
Function and homology information


asparaginyl-tRNA synthase (glutamine-hydrolyzing) activity / glutaminyl-tRNA synthase (glutamine-hydrolysing) / glutamyl-tRNA(Gln) amidotransferase complex / Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor / glutaminyl-tRNAGln biosynthesis via transamidation / glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity / regulation of translational fidelity / translation / ATP binding
Similarity search - Function
Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase superfamily, subunit C / Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase C subunit, N-terminal domain / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1 / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit / Glutamyl-tRNA(Gln) amidotransferase A subunit / Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic / Glutamyl-tRNA(Gln) amidotransferase, subunit B, conserved site / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, subunit B /E ...Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase superfamily, subunit C / Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase C subunit, N-terminal domain / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1 / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit / Glutamyl-tRNA(Gln) amidotransferase A subunit / Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic / Glutamyl-tRNA(Gln) amidotransferase, subunit B, conserved site / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, subunit B /E / GatB/GatE catalytic domain / Glutamyl-tRNA(Gln) amidotransferase subunit B signature. / Asn/Gln amidotransferase / GatB domain / GatB domain / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 2 / Aspartyl/glutamyl-tRNA amidotransferase subunit B-like / Amidase / Amidase, conserved site / Amidases signature. / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Glutamine synthetase/guanido kinase, catalytic domain / Histone, subunit A / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ASPARAGINE / Glutamyl-tRNA(Gln) amidotransferase subunit A / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B / Glutamyl-tRNA(Gln) amidotransferase subunit C
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWu, J. / Bu, W. / Sheppard, K. / Kitabatake, M. / Soll, D. / Smith, J.L.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Insights into tRNA-Dependent Amidotransferase Evolution and Catalysis from the Structure of the Aquifex aeolicus Enzyme
Authors: Wu, J. / Bu, W. / Sheppard, K. / Kitabatake, M. / Kwon, S.T. / Soll, D. / Smith, J.L.
History
DepositionApr 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamyl-tRNA(Gln) amidotransferase subunit A
B: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
C: Glutamyl-tRNA(Gln) amidotransferase subunit C
D: Glutamyl-tRNA(Gln) amidotransferase subunit A
E: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
F: Glutamyl-tRNA(Gln) amidotransferase subunit C
G: Glutamyl-tRNA(Gln) amidotransferase subunit A
H: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
I: Glutamyl-tRNA(Gln) amidotransferase subunit C
J: Glutamyl-tRNA(Gln) amidotransferase subunit A
K: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
L: Glutamyl-tRNA(Gln) amidotransferase subunit C
M: Glutamyl-tRNA(Gln) amidotransferase subunit A
N: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
O: Glutamyl-tRNA(Gln) amidotransferase subunit C
P: Glutamyl-tRNA(Gln) amidotransferase subunit A
Q: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
R: Glutamyl-tRNA(Gln) amidotransferase subunit C
S: Glutamyl-tRNA(Gln) amidotransferase subunit A
T: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
U: Glutamyl-tRNA(Gln) amidotransferase subunit C
V: Glutamyl-tRNA(Gln) amidotransferase subunit A
W: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
X: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)964,76456
Polymers959,57124
Non-polymers5,19232
Water00
1
A: Glutamyl-tRNA(Gln) amidotransferase subunit A
B: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
C: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5957
Polymers119,9463
Non-polymers6494
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-79 kcal/mol
Surface area39390 Å2
MethodPISA
2
D: Glutamyl-tRNA(Gln) amidotransferase subunit A
E: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
F: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5957
Polymers119,9463
Non-polymers6494
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11830 Å2
ΔGint-80 kcal/mol
Surface area39190 Å2
MethodPISA
3
G: Glutamyl-tRNA(Gln) amidotransferase subunit A
H: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
I: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5957
Polymers119,9463
Non-polymers6494
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11870 Å2
ΔGint-81 kcal/mol
Surface area39060 Å2
MethodPISA
4
J: Glutamyl-tRNA(Gln) amidotransferase subunit A
K: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
L: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5957
Polymers119,9463
Non-polymers6494
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11740 Å2
ΔGint-79 kcal/mol
Surface area39240 Å2
MethodPISA
5
M: Glutamyl-tRNA(Gln) amidotransferase subunit A
N: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
O: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5957
Polymers119,9463
Non-polymers6494
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-79 kcal/mol
Surface area39230 Å2
MethodPISA
6
P: Glutamyl-tRNA(Gln) amidotransferase subunit A
Q: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
R: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5957
Polymers119,9463
Non-polymers6494
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-76 kcal/mol
Surface area39110 Å2
MethodPISA
7
S: Glutamyl-tRNA(Gln) amidotransferase subunit A
T: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
U: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5957
Polymers119,9463
Non-polymers6494
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11830 Å2
ΔGint-85 kcal/mol
Surface area39240 Å2
MethodPISA
8
V: Glutamyl-tRNA(Gln) amidotransferase subunit A
W: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
X: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5957
Polymers119,9463
Non-polymers6494
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-77 kcal/mol
Surface area39300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.482, 131.012, 154.668
Angle α, β, γ (deg.)90.02, 90.00, 89.91
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31G
41J
51M
61P
71S
81V
12B
22E
32H
42K
52N
62Q
72T
82W
13B
23E
33H
43K
53N
63Q
73T
83W
14C
24F
34I
44L
54O
64R
74U
84X

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTHRTHRAA1 - 4781 - 478
21METMETTHRTHRDD1 - 4781 - 478
31METMETTHRTHRGG1 - 4781 - 478
41METMETTHRTHRJJ1 - 4781 - 478
51METMETTHRTHRMM1 - 4781 - 478
61METMETTHRTHRPP1 - 4781 - 478
71METMETTHRTHRSS1 - 4781 - 478
81METMETTHRTHRVV1 - 4781 - 478
12GLUGLULYSLYSBB3 - 2933 - 293
22GLUGLULYSLYSEE3 - 2933 - 293
32GLUGLULYSLYSHH3 - 2933 - 293
42GLUGLULYSLYSKK3 - 2933 - 293
52GLUGLULYSLYSNN3 - 2933 - 293
62GLUGLULYSLYSQQ3 - 2933 - 293
72GLUGLULYSLYSTT3 - 2933 - 293
82GLUGLULYSLYSWW3 - 2933 - 293
13ASNASNLEULEUBB294 - 412294 - 412
23ASNASNLEULEUEE294 - 412294 - 412
33ASNASNLEULEUHH294 - 412294 - 412
43ASNASNLEULEUKK294 - 412294 - 412
53ASNASNLEULEUNN294 - 412294 - 412
63ASNASNLEULEUQQ294 - 412294 - 412
73ASNASNLEULEUTT294 - 412294 - 412
83ASNASNLEULEUWW294 - 412294 - 412
14VALVALVALVALCC2 - 922 - 92
24VALVALVALVALFF2 - 922 - 92
34VALVALVALVALII2 - 922 - 92
44VALVALVALVALLL2 - 922 - 92
54VALVALVALVALOO2 - 922 - 92
64VALVALVALVALRR2 - 922 - 92
74VALVALVALVALUU2 - 922 - 92
84VALVALVALVALXX2 - 922 - 92

NCS ensembles :
ID
1
2
3
4

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Components

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Glutamyl-tRNA(Gln) amidotransferase subunit ... , 2 types, 16 molecules ADGJMPSVCFILORUX

#1: Protein
Glutamyl-tRNA(Gln) amidotransferase subunit A / Glu-ADT subunit A


Mass: 53589.160 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_247, gatA, GATCA / Plasmid: pET17b-CA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O66610, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor
#3: Protein
Glutamyl-tRNA(Gln) amidotransferase subunit C / Glu-ADT subunit C


Mass: 11228.740 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: gatC, aq_2149 / Plasmid: pET17b-CA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O67904, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor

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Protein , 1 types, 8 molecules BEHKNQTW

#2: Protein
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B / Asp/Glu-ADT subunit B


Mass: 55128.535 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_461, gatB / Plasmid: pET17b-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O66766, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor

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Non-polymers , 4 types, 32 molecules

#4: Chemical
ChemComp-ASN / ASPARAGINE


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H8N2O3
#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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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: 3

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1:1 ratio of Protein solution (6-9mg/ml GatCAB,10mM HEPES, 50uM Zn acetate,10mM Asn, 0.6mM ATP) mix with well solution (10-12% PEG3350, 10mM Mg formate), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D11.0274,0.9804
SYNCHROTRONAPS 23-ID-D20.97934
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDMar 24, 2006MONOCHROMATOR: MIRRORS
MARMOSAIC 300 mm CCD2CCDMar 20, 2007MONOCHROMATOR: MIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MIRRORSMADMx-ray1
2MIRRORSSINGLE WAVELENGTHx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.02741
20.98041
30.979341
ReflectionResolution: 2.3→40.5 Å / Num. all: 405875 / Num. obs: 405875 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 11.5
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.347 / % possible all: 73.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2GI3 and 2G5H

2gi3

2g5h


Resolution: 2.3→40.5 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.923 / SU B: 11.215 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 0.408 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2726 20322 5 %RANDOM
Rwork0.24004 ---
obs0.24169 385553 91.69 %-
all-405875 --
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: 50.929 Å2
Baniso -1Baniso -2Baniso -3
1--4.63 Å2-0.01 Å2-0.26 Å2
2--9.07 Å20.04 Å2
3----4.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.198 Å0.359 Å
Refinement stepCycle: LAST / Resolution: 2.3→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms62848 0 296 0 63144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02264481
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.98987106
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14957808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07224.4962936
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.6561511946
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.93315400
X-RAY DIFFRACTIONr_chiral_restr0.0940.29520
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0248240
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.230945
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.243623
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.22694
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0980.215
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.2122
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6721.540352
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11263456
X-RAY DIFFRACTIONr_scbond_it1.454327450
X-RAY DIFFRACTIONr_scangle_it2.3054.523650
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
11A1904tight positional0.040.05
12D1904tight positional0.030.05
13G1904tight positional0.030.05
14J1904tight positional0.030.05
15M1904tight positional0.030.05
16P1904tight positional0.040.05
17S1904tight positional0.040.05
18V1904tight positional0.040.05
21B1164tight positional0.040.05
22E1164tight positional0.030.05
23H1164tight positional0.040.05
24K1164tight positional0.040.05
25N1164tight positional0.030.05
26Q1164tight positional0.040.05
27T1164tight positional0.030.05
28W1164tight positional0.030.05
31B476tight positional0.020.05
32E476tight positional0.020.05
33H476tight positional0.030.05
34K476tight positional0.030.05
35N476tight positional0.020.05
36Q476tight positional0.020.05
37T476tight positional0.020.05
38W476tight positional0.020.05
41C364tight positional0.030.05
42F364tight positional0.030.05
43I364tight positional0.030.05
44L364tight positional0.030.05
45O364tight positional0.030.05
46R364tight positional0.030.05
47U364tight positional0.030.05
48X364tight positional0.030.05
11A1864medium positional0.340.5
12D1864medium positional0.340.5
13G1864medium positional0.340.5
14J1864medium positional0.340.5
15M1864medium positional0.340.5
16P1864medium positional0.340.5
17S1864medium positional0.350.5
18V1864medium positional0.330.5
21B1187medium positional0.370.5
22E1187medium positional0.350.5
23H1187medium positional0.370.5
24K1187medium positional0.360.5
25N1187medium positional0.370.5
26Q1187medium positional0.380.5
27T1187medium positional0.370.5
28W1187medium positional0.350.5
31B481medium positional0.350.5
32E481medium positional0.360.5
33H481medium positional0.350.5
34K481medium positional0.370.5
35N481medium positional0.320.5
36Q481medium positional0.360.5
37T481medium positional0.330.5
38W481medium positional0.380.5
41C400medium positional0.410.5
42F400medium positional0.370.5
43I400medium positional0.360.5
44L400medium positional0.360.5
45O400medium positional0.350.5
46R400medium positional0.560.5
47U400medium positional0.390.5
48X400medium positional0.340.5
11A1904tight thermal0.090.5
12D1904tight thermal0.090.5
13G1904tight thermal0.090.5
14J1904tight thermal0.10.5
15M1904tight thermal0.090.5
16P1904tight thermal0.10.5
17S1904tight thermal0.10.5
18V1904tight thermal0.090.5
21B1164tight thermal0.070.5
22E1164tight thermal0.090.5
23H1164tight thermal0.070.5
24K1164tight thermal0.090.5
25N1164tight thermal0.070.5
26Q1164tight thermal0.090.5
27T1164tight thermal0.090.5
28W1164tight thermal0.070.5
31B476tight thermal0.040.5
32E476tight thermal0.050.5
33H476tight thermal0.040.5
34K476tight thermal0.040.5
35N476tight thermal0.040.5
36Q476tight thermal0.040.5
37T476tight thermal0.050.5
38W476tight thermal0.040.5
41C364tight thermal0.070.5
42F364tight thermal0.070.5
43I364tight thermal0.060.5
44L364tight thermal0.070.5
45O364tight thermal0.070.5
46R364tight thermal0.080.5
47U364tight thermal0.070.5
48X364tight thermal0.070.5
11A1864medium thermal0.642
12D1864medium thermal0.662
13G1864medium thermal0.612
14J1864medium thermal0.682
15M1864medium thermal0.622
16P1864medium thermal0.692
17S1864medium thermal0.622
18V1864medium thermal0.672
21B1187medium thermal0.572
22E1187medium thermal0.612
23H1187medium thermal0.552
24K1187medium thermal0.652
25N1187medium thermal0.562
26Q1187medium thermal0.682
27T1187medium thermal0.622
28W1187medium thermal0.592
31B481medium thermal0.352
32E481medium thermal0.372
33H481medium thermal0.322
34K481medium thermal0.352
35N481medium thermal0.282
36Q481medium thermal0.322
37T481medium thermal0.372
38W481medium thermal0.322
41C400medium thermal0.512
42F400medium thermal0.492
43I400medium thermal0.462
44L400medium thermal0.572
45O400medium thermal0.482
46R400medium thermal0.612
47U400medium thermal0.52
48X400medium thermal0.542
LS refinement shellResolution: 2.3→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 1185 -
Rwork0.337 22441 -
obs--72.25 %

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