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- PDB-3h0r: Structure of trna-dependent amidotransferase gatcab from aquifex ... -

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Basic information

Entry
Database: PDB / ID: 3h0r
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 / ASPARTIC ACID / ADENOSINE-5'-TRIPHOSPHATE / : / 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: 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 10, 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_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.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_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

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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)966,19466
Polymers959,57124
Non-polymers6,62342
Water88349
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)120,6818
Polymers119,9463
Non-polymers7355
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-79 kcal/mol
Surface area39330 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)120,7618
Polymers119,9463
Non-polymers8155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12100 Å2
ΔGint-77 kcal/mol
Surface area39380 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)120,8949
Polymers119,9463
Non-polymers9486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12080 Å2
ΔGint-80 kcal/mol
Surface area38960 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)120,7618
Polymers119,9463
Non-polymers8155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12100 Å2
ΔGint-78 kcal/mol
Surface area39150 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)120,8949
Polymers119,9463
Non-polymers9486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12130 Å2
ΔGint-83 kcal/mol
Surface area39210 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)120,7618
Polymers119,9463
Non-polymers8155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12040 Å2
ΔGint-80 kcal/mol
Surface area39180 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)120,6818
Polymers119,9463
Non-polymers7355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12020 Å2
ΔGint-84 kcal/mol
Surface area39340 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)120,7618
Polymers119,9463
Non-polymers8155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12090 Å2
ΔGint-79 kcal/mol
Surface area39290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.377, 130.411, 153.973
Angle α, β, γ (deg.)89.89, 90.21, 89.95
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

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTHRTHR3AA1 - 4781 - 478
21METMETTHRTHR3DD1 - 4781 - 478
31METMETTHRTHR3GG1 - 4781 - 478
41METMETTHRTHR3JJ1 - 4781 - 478
51METMETTHRTHR3MM1 - 4781 - 478
61METMETTHRTHR3PP1 - 4781 - 478
71METMETTHRTHR3SS1 - 4781 - 478
81METMETTHRTHR3VV1 - 4781 - 478
12GLUGLULYSLYS4BB3 - 2933 - 293
22GLUGLULYSLYS4EE3 - 2933 - 293
32GLUGLULYSLYS4HH3 - 2933 - 293
42GLUGLULYSLYS4KK3 - 2933 - 293
52GLUGLULYSLYS4NN3 - 2933 - 293
62GLUGLULYSLYS4QQ3 - 2933 - 293
72GLUGLULYSLYS4TT3 - 2933 - 293
82GLUGLULYSLYS4WW3 - 2933 - 293
13ASNASNLEULEU4BB294 - 412294 - 412
23ASNASNLEULEU4EE294 - 412294 - 412
33ASNASNLEULEU4HH294 - 412294 - 412
43ASNASNLEULEU4KK294 - 412294 - 412
53ASNASNLEULEU4NN294 - 412294 - 412
63ASNASNLEULEU4QQ294 - 412294 - 412
73ASNASNLEULEU4TT294 - 412294 - 412
83ASNASNLEULEU4WW294 - 412294 - 412
14VALVALVALVAL4CC2 - 922 - 92
24VALVALVALVAL4FF2 - 922 - 92
34VALVALVALVAL4II2 - 922 - 92
44VALVALVALVAL4LL2 - 922 - 92
54VALVALVALVAL4OO2 - 922 - 92
64VALVALVALVAL4RR2 - 922 - 92
74VALVALVALVAL4UU2 - 922 - 92
84VALVALVALVAL4XX2 - 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 / Asp/Glu-ADT subunit B


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: aq_2149, gatC / 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


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

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Non-polymers , 7 types, 91 molecules

#4: Chemical
ChemComp-ASN / ASPARAGINE / Glu-ADT subunit C


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H8N2O3
References: Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mn
#8: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#9: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
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), crystal soaked in the mother liquor ...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), crystal soaked in the mother liquor with 10mMAsn, 10mM Asp, 10mM ATP, 10mM MnCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3→49 Å / Num. all: 232054 / Num. obs: 182013 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 5.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.71 / % possible all: 84.5

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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 entry 3H0L

3h0l


Resolution: 3→48.97 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.88 / SU B: 31.804 / SU ML: 0.55 / Cross valid method: THROUGHOUT / ESU R Free: 0.56 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30604 9614 5 %RANDOM
Rwork0.26299 ---
obs0.26515 180942 96.04 %-
all-190557 --
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: 60.397 Å2
Baniso -1Baniso -2Baniso -3
1--6.41 Å2-0.08 Å2-0.15 Å2
2--14.03 Å2-0.1 Å2
3----7.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.412 Å0.492 Å
Refinement stepCycle: LAST / Resolution: 3→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms62912 0 282 49 63243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02264621
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9987270
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55657808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07724.472922
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.7221511885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.73115400
X-RAY DIFFRACTIONr_chiral_restr0.1010.29522
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0248280
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.230670
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.243564
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.22045
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.2182
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
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
11A1912tight positional0.040.05
12D1912tight positional0.040.05
13G1912tight positional0.030.05
14J1912tight positional0.040.05
15M1912tight positional0.040.05
16P1912tight positional0.040.05
17S1912tight positional0.040.05
18V1912tight positional0.040.05
21B2349medium positional0.290.5
22E2349medium positional0.270.5
23H2349medium positional0.290.5
24K2349medium positional0.280.5
25N2349medium positional0.280.5
26Q2349medium positional0.310.5
27T2349medium positional0.290.5
28W2349medium positional0.270.5
31B949medium positional0.270.5
32E949medium positional0.280.5
33H949medium positional0.30.5
34K949medium positional0.290.5
35N949medium positional0.30.5
36Q949medium positional0.320.5
37T949medium positional0.280.5
38W949medium positional0.280.5
41C760medium positional0.270.5
42F760medium positional0.310.5
43I760medium positional0.270.5
44L760medium positional0.30.5
45O760medium positional0.310.5
46R760medium positional0.330.5
47U760medium positional0.290.5
48X760medium positional0.280.5
11A1876loose positional0.355
12D1876loose positional0.375
13G1876loose positional0.385
14J1876loose positional0.415
15M1876loose positional0.365
16P1876loose positional0.375
17S1876loose positional0.385
18V1876loose positional0.385
LS refinement shellResolution: 3→3.162 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.393 1328 -
Rwork0.373 25280 -
obs--91.88 %

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