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- PDB-2wgm: Complete ion-coordination structure in the rotor ring of Na-depen... -

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Basic information

Entry
Database: PDB / ID: 2wgm
TitleComplete ion-coordination structure in the rotor ring of Na-dependent F-ATP synthase
ComponentsATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
KeywordsMEMBRANE PROTEIN / F1FO-ATP SYNTHASE ROTOR / SODIUM-MOTIVE FORCE / CELL INNER MEMBRANE CF(0) / TRANSPORT / LIPID-BINDING / ION COORDINATION AND SELECTIVITY / HYDROGEN ION TRANSPORT / TRANSMEMBRANE / C-RING STRUCTURE / SODIUM TRANSPORT / CELL MEMBRANE / ATP SYNTHESIS
Function / homology
Function and homology information


sodium ion transport / proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / plasma membrane
Similarity search - Function
F1F0 ATP synthase subunit C / F1FO ATP Synthase / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit C / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NONAN-1-OL / ATP synthase subunit c, sodium ion specific
Similarity search - Component
Biological speciesILYOBACTER TARTARICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMeier, T. / Pogoryelov, D. / Diederichs, K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Complete Ion-Coordination Structure in the Rotor Ring of Na(+)-Dependent F-ATP Synthases.
Authors: Meier, T. / Krah, A. / Bond, P.J. / Pogoryelov, D. / Diederichs, K. / Faraldo-Gomez, J.D.
History
DepositionApr 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
B: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
C: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
D: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
E: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
F: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
G: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
H: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
I: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
J: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
K: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
L: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
M: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
N: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
O: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
P: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
Q: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
R: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
S: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
T: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
U: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
V: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
a: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
b: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
c: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
d: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
e: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
f: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
g: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
h: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
i: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
j: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
k: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
l: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
m: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
n: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
o: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
p: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
q: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
r: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
s: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
t: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
u: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
v: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)394,528132
Polymers387,16944
Non-polymers7,35988
Water7,440413
1
a: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
b: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
c: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
d: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
e: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
f: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
g: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
h: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
i: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
j: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
k: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,63233
Polymers96,79211
Non-polymers1,84022
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47390 Å2
ΔGint-479 kcal/mol
Surface area25010 Å2
MethodPISA
2
l: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
m: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
n: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
o: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
p: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
q: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
r: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
s: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
t: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
u: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
v: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,63233
Polymers96,79211
Non-polymers1,84022
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47490 Å2
ΔGint-475.9 kcal/mol
Surface area24960 Å2
MethodPISA
3
A: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
B: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
C: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
D: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
E: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
F: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
G: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
H: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
I: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
J: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
K: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,63233
Polymers96,79211
Non-polymers1,84022
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47540 Å2
ΔGint-476.7 kcal/mol
Surface area24890 Å2
MethodPISA
4
L: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
M: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
N: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
O: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
P: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
Q: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
R: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
S: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
T: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
U: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
V: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,63233
Polymers96,79211
Non-polymers1,84022
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47530 Å2
ΔGint-473.9 kcal/mol
Surface area24970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.690, 139.280, 151.910
Angle α, β, γ (deg.)90.00, 118.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201
211
221
231
241
251
261
271
281
291
301
311
321
331
341
351
361
371
381
391
401
411
421
431
441

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
211CHAIN B AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
311CHAIN C AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
411CHAIN D AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
511CHAIN E AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
611CHAIN F AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
711CHAIN G AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
811CHAIN H AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
911CHAIN I AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1011CHAIN J AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1111CHAIN K AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1211CHAIN L AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1311CHAIN M AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1411CHAIN N AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1511CHAIN O AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1611CHAIN P AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1711CHAIN Q AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1811CHAIN R AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1911CHAIN S AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2011CHAIN T AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2111CHAIN U AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2211CHAIN V AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2311CHAIN a AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2411CHAIN b AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2511CHAIN c AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2611CHAIN d AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2711CHAIN e AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2811CHAIN f AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2911CHAIN g AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3011CHAIN h AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3111CHAIN i AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3211CHAIN j AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3311CHAIN k AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3411CHAIN l AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3511CHAIN m AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3611CHAIN n AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3711CHAIN o AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3811CHAIN p AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3911CHAIN q AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
4011CHAIN r AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
4111CHAIN s AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
4211CHAIN t AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
4311CHAIN u AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
4411CHAIN v AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)

NCS oper: (Code: given
Matrix: (0.994071, 0.037842, 0.101931), (0.022885, 0.843657, -0.536395), (-0.106293, 0.535547, 0.837789)
Vector: -2.8298, 13.8727, -8.73288)

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Components

#1: Protein ...
ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC / / C11 RING / ATP SYNTHASE F(0) SECTOR SUBUNIT C / F-TYPE ATPASE SUBUNIT C / LIPID-BINDING PROTEIN / F- ...C11 RING / ATP SYNTHASE F(0) SECTOR SUBUNIT C / F-TYPE ATPASE SUBUNIT C / LIPID-BINDING PROTEIN / F-ATPASE SUBUNIT C


Mass: 8799.304 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) ILYOBACTER TARTARICUS (bacteria) / Strain: 2382 / References: UniProt: Q8KRV3
#2: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: Na
#3: Chemical...
ChemComp-F09 / NONAN-1-OL / 1-Nonanol


Mass: 144.254 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: C9H20O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 66.1 % / Description: NONE
Crystal growpH: 4.5 / Details: pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 2.35→40 Å / Num. obs: 220545 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 39.81 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.8
Reflection shellResolution: 2.35→2.45 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 1.8 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YCE

1yce


Resolution: 2.35→39.678 Å / SU ML: 0 / σ(F): 1.99 / Phase error: 29.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2451 10959 5 %
Rwork0.2203 --
obs0.2215 219965 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.877 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso mean: 60.4 Å2
Baniso -1Baniso -2Baniso -3
1--22.873 Å20 Å20.9992 Å2
2--16.2039 Å20 Å2
3---6.6691 Å2
Refinement stepCycle: LAST / Resolution: 2.35→39.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27104 0 484 413 28001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01257464
X-RAY DIFFRACTIONf_angle_d0.704104456
X-RAY DIFFRACTIONf_dihedral_angle_d13.36713860
X-RAY DIFFRACTIONf_chiral_restr0.0534664
X-RAY DIFFRACTIONf_plane_restr0.0028624
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A582X-RAY DIFFRACTIONPOSITIONAL
12B582X-RAY DIFFRACTIONPOSITIONAL0.06
13C582X-RAY DIFFRACTIONPOSITIONAL0.032
14D582X-RAY DIFFRACTIONPOSITIONAL0.036
15E582X-RAY DIFFRACTIONPOSITIONAL0.034
16F582X-RAY DIFFRACTIONPOSITIONAL0.035
17G582X-RAY DIFFRACTIONPOSITIONAL0.035
18H582X-RAY DIFFRACTIONPOSITIONAL0.036
19I582X-RAY DIFFRACTIONPOSITIONAL0.034
110J582X-RAY DIFFRACTIONPOSITIONAL0.036
111K582X-RAY DIFFRACTIONPOSITIONAL0.043
112L582X-RAY DIFFRACTIONPOSITIONAL0.03
113M582X-RAY DIFFRACTIONPOSITIONAL0.034
114N582X-RAY DIFFRACTIONPOSITIONAL0.031
115O582X-RAY DIFFRACTIONPOSITIONAL0.029
116P582X-RAY DIFFRACTIONPOSITIONAL0.031
117Q582X-RAY DIFFRACTIONPOSITIONAL0.03
118R582X-RAY DIFFRACTIONPOSITIONAL0.032
119S582X-RAY DIFFRACTIONPOSITIONAL0.034
120T582X-RAY DIFFRACTIONPOSITIONAL0.036
121U582X-RAY DIFFRACTIONPOSITIONAL0.037
122V582X-RAY DIFFRACTIONPOSITIONAL0.034
123A582X-RAY DIFFRACTIONPOSITIONAL0.027
124B582X-RAY DIFFRACTIONPOSITIONAL0.034
125C582X-RAY DIFFRACTIONPOSITIONAL0.033
126D582X-RAY DIFFRACTIONPOSITIONAL0.032
127E582X-RAY DIFFRACTIONPOSITIONAL0.03
128F582X-RAY DIFFRACTIONPOSITIONAL0.03
129G582X-RAY DIFFRACTIONPOSITIONAL0.032
130H582X-RAY DIFFRACTIONPOSITIONAL0.034
131I582X-RAY DIFFRACTIONPOSITIONAL0.034
132J582X-RAY DIFFRACTIONPOSITIONAL0.038
133K582X-RAY DIFFRACTIONPOSITIONAL0.037
134L582X-RAY DIFFRACTIONPOSITIONAL0.028
135M582X-RAY DIFFRACTIONPOSITIONAL0.035
136N582X-RAY DIFFRACTIONPOSITIONAL0.035
137O582X-RAY DIFFRACTIONPOSITIONAL0.033
138P582X-RAY DIFFRACTIONPOSITIONAL0.036
139Q582X-RAY DIFFRACTIONPOSITIONAL0.039
140R582X-RAY DIFFRACTIONPOSITIONAL0.035
141S582X-RAY DIFFRACTIONPOSITIONAL0.033
142T582X-RAY DIFFRACTIONPOSITIONAL0.037
143U582X-RAY DIFFRACTIONPOSITIONAL0.036
144V582X-RAY DIFFRACTIONPOSITIONAL0.033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.37670.38273070.34036073X-RAY DIFFRACTION86
2.3767-2.40470.34613260.32226424X-RAY DIFFRACTION91
2.4047-2.4340.3663270.32186582X-RAY DIFFRACTION94
2.434-2.46480.34413620.30046838X-RAY DIFFRACTION97
2.4648-2.49720.31783730.28497027X-RAY DIFFRACTION100
2.4972-2.53140.31963290.26197077X-RAY DIFFRACTION100
2.5314-2.56760.28523420.24967018X-RAY DIFFRACTION100
2.5676-2.60590.27983750.23617016X-RAY DIFFRACTION100
2.6059-2.64660.26633660.23087045X-RAY DIFFRACTION100
2.6466-2.690.25113830.22556974X-RAY DIFFRACTION100
2.69-2.73640.26743500.22417057X-RAY DIFFRACTION100
2.7364-2.78610.24283730.21797022X-RAY DIFFRACTION100
2.7861-2.83970.26643730.21676992X-RAY DIFFRACTION100
2.8397-2.89760.25243530.20317023X-RAY DIFFRACTION100
2.8976-2.96060.25193490.20857039X-RAY DIFFRACTION100
2.9606-3.02950.21943910.21157004X-RAY DIFFRACTION99
3.0295-3.10520.24943660.2097052X-RAY DIFFRACTION100
3.1052-3.18910.24433810.21477016X-RAY DIFFRACTION100
3.1891-3.28290.24744060.22626979X-RAY DIFFRACTION100
3.2829-3.38880.27573770.2227069X-RAY DIFFRACTION100
3.3888-3.50990.23693520.22797022X-RAY DIFFRACTION100
3.5099-3.65030.243440.20757108X-RAY DIFFRACTION100
3.6503-3.81630.22524070.20437042X-RAY DIFFRACTION100
3.8163-4.01730.24163840.20547030X-RAY DIFFRACTION100
4.0173-4.26880.22043370.19777091X-RAY DIFFRACTION100
4.2688-4.59790.20493860.19227065X-RAY DIFFRACTION100
4.5979-5.05980.21894100.19647059X-RAY DIFFRACTION100
5.0598-5.790.23573640.21577073X-RAY DIFFRACTION100
5.79-7.28740.19133920.18227131X-RAY DIFFRACTION100
7.2874-39.68340.20873740.21427058X-RAY DIFFRACTION98
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)
1-0.4142-0.3669-0.26980.79140.12130.4566-0.0487-0.14640.24970.01550.0626-0.03140.00560.0569-0.03340.2440.0074-0.01460.27050.03760.21497.471211.749732.6749
23.2209-0.42260.04470.806-0.20860.5962-0.2354-0.93140.4372-0.01660.07670.035-0.12670.1020.10160.3193-0.0047-0.03580.4022-0.08420.28145.779220.778136.8354
31.0499-0.5536-0.0601-0.0203-0.42180.6049-0.2785-0.08220.83030.02940.1610.0417-0.1120.00560.09390.3333-0.0125-0.00210.2351-0.21140.56023.89730.538335.4143
42.27050.1360.7335-0.5971-0.22420.7607-0.0429-0.13651.7298-0.0960.00460.2528-0.1620.03330.04920.3399-0.04490.00530.2209-0.15930.98712.422637.981128.8252
50.3618-0.59230.01070.51660.350.8497-0.22120.01081.1989-0.13360.0861-0.0418-0.09580.06760.08710.3599-0.0332-0.00270.14310.09980.87231.776340.728919.1934
60.71370.172-0.07071.07690.35651.2644-0.09430.56431.1385-0.09450.08430.0283-0.08060.1345-0.00440.3523-0.0062-0.00260.28080.29010.80752.178737.92569.5756
70.0576-0.692-0.60220.86470.1290.8679-0.00560.56620.2379-0.0966-0.016-0.16830.0431-0.01160.03020.3563-0.04390.00540.50490.26910.46343.560730.4482.9732
82.0906-0.1982-0.43620.7254-0.30831.0076-0.27460.91730.6129-0.12440.1626-0.0244-0.00190.23180.10040.3213-0.03490.01530.57620.13480.34365.397720.6951.5451
90.689-0.37330.4520.64960.01870.6553-0.25950.48370.0214-0.0460.0907-0.0586-0.01540.15670.10370.3271-0.02590.03650.4431-0.01920.28937.161511.74065.6764
101.8669-1.27640.14420.28910.13261.2123-0.12430.2185-0.2665-0.05160.107-0.15770.0620.2056-0.01990.32480.02580.03490.2862-0.05660.38498.27986.465314.1721
111.1803-0.7126-0.180.27610.44110.5877-0.1726-0.1531-0.31320.04840.07530.08040.04380.06090.08490.31320.02020.00430.23940.09840.37098.3946.424724.209
120.6683-0.1699-0.87620.6013-0.50841.01120.0014-0.28450.1433-0.00530.0338-0.04030.02360.0114-0.02990.28970.0140.00620.1754-0.13450.4052-69.908422.510531.9134
131.24010.05350.20470.9112-0.04391.0350.0363-0.62280.31620.0216-0.0437-0.03440.0355-0.0704-0.00870.2482-0.0073-0.01380.2826-0.0710.2132-68.238314.119537.2551
140.75530.1304-0.04460.64950.05630.8685-0.161-0.1565-0.1385-0.01910.0907-0.00840.0701-0.19740.05930.2828-0.0214-0.01250.23210.07010.211-66.36494.268537.122
15-0.00520.7113-0.3166-0.0241-0.06090.9553-0.21570.0482-0.3035-0.06260.12180.01660.1202-0.04140.07070.3224-0.02540.01320.11920.11150.4534-64.8881-3.986231.5549
16-1.26150.6869-0.0460.579-0.20181.0412-0.0720.2736-0.1332-0.10690.082-0.0563-0.0419-0.0692-0.01680.333-0.0170.00680.1591-0.01620.4834-64.2384-7.946622.3794
17-0.30990.01290.25140.4617-0.22771.3496-0.07560.1611-0.2738-0.19680.0620.08150.0677-0.0339-0.00540.3561-0.0440.01120.2184-0.10770.4255-64.645-6.475412.4837
180.5404-0.72640.12390.7064-0.0620.3395-0.0750.7937-0.2225-0.11360.0785-0.0107-0.0034-0.1602-0.03870.3348-0.08460.00270.5233-0.10480.2155-65.96450.04694.9472
190.5175-0.4634-0.23890.5824-0.01460.5408-0.16060.94780.0718-0.11020.17110.0354-0.0568-0.1411-0.02170.3578-0.0452-0.00150.57580.03930.2224-67.83839.53372.2576
201.48550.0949-0.22740.8737-0.16631.0074-0.23180.72050.5572-0.02430.20260.0181-0.0471-0.21830.00470.3064-0.00340.00020.51740.15130.3314-69.581318.98165.1414
210.6437-1.1037-0.49480.3838-0.11891.11420.00660.23890.7072-0.0409-0.00930.1705-0.059-0.0497-0.04120.32210.0316-0.02040.26660.15150.5778-70.730625.331412.8576
222.108-0.1948-0.21460.3684-0.23041.3429-0.197-0.09781.19920.04520.1046-0.1228-0.1154-0.10580.0580.3270.0373-0.01030.1158-0.03280.6042-70.829126.665722.8215
230.8613-0.59210.68621.15490.50530.7171-0.0339-0.8412-0.37330.09280.06220.0718-0.03-0.0279-0.01060.27920.0372-0.02290.3580.21420.292233.800678.67460.1167
241.7804-0.53120.17510.7613-0.2340.24980.0445-1.03910.01520.072-0.07360.0081-0.02870.04670.00940.3444-0.0352-0.02180.54710.08070.275532.104587.602664.473
252.8666-0.24491.2540.3394-0.20681.0237-0.0869-0.87460.19850.0494-0.00470.0428-0.11820.01260.05570.3362-0.0352-0.00510.428-0.07040.30330.204297.404363.2502
26-0.1790.3157-0.50990.8902-0.1380.9899-0.155-0.18050.6278-0.07580.06390.0454-0.12070.05130.04780.3505-0.0355-0.00760.2398-0.0980.460528.7267104.968756.8009
270.71970.5223-0.15890.21870.04150.5996-0.0173-0.11790.8124-0.0656-0.01060.2201-0.11060.00870.04050.3986-0.0661-0.03830.20090.01060.535628.0925107.936247.2214
280.30360.4401-0.47860.78490.23670.3503-0.04670.20330.1885-0.10870.0690.00650.0094-0.0389-0.01020.344-0.0375-0.02590.22280.13580.420928.4973105.312237.559
29-0.8441-0.195-1.28971.2852-0.23780.3033-0.09910.5062-0.1095-0.03160.0721-0.0194-0.0054-0.0593-0.00090.3155-0.0677-0.00670.40860.09540.250929.875397.974830.8369
301.6077-0.4319-0.32110.83610.08830.8157-0.17450.6787-0.0264-0.03460.12990.12270.04520.06190.03660.3122-0.0397-0.00590.3364-0.01750.221231.735188.253129.1773
310.9082-0.26580.3480.21940.23150.8055-0.15720.1801-0.684-0.06310.0756-0.02320.08650.10180.04990.3749-0.01860.01160.322-0.11920.492833.505979.215433.0961
320.5699-0.18340.0873-0.00730.0960.5815-0.26310.0771-0.6020.08010.13810.0170.08650.03140.08790.34910.00860.01990.1939-0.00750.66934.6373.747741.5114
331.34970.4062-0.64210.4560.02191.2287-0.1585-0.3889-0.89480.00350.09820.07270.04910.1610.02990.3350.0381-0.00170.23480.11550.641634.724973.540751.5459
341.0595-0.6969-0.64070.6404-0.27990.54660.0119-0.5108-0.03780.0510.05050.0001-0.0098-0.0597-0.05650.29080.0077-0.0150.3413-0.00570.2696-43.615489.485259.5979
351.6667-0.6048-0.3091.21350.36020.5489-0.0038-0.997-0.50250.0617-0.0012-0.05930.1151-0.04680.01880.3083-0.0128-0.03710.48240.16940.2211-41.922280.992564.7598
360.0394-0.5846-0.01671.03780.21.4652-0.0937-0.8856-0.61590.10250.0606-0.00430.1852-0.0156-0.01510.33150.00860.0150.47160.30240.5596-40.039471.110364.4031
370.6220.1385-0.919-0.08810.12681.168-0.1668-0.2769-1.55690.01850.0434-0.13340.216-0.13260.08290.3506-0.0254-0.00750.33060.26830.9872-38.510162.985558.701
38-0.33430.21390.35180.8364-0.2041.2445-0.1687-0.2998-1.1062-0.13030.09840.19880.2182-0.18930.08520.3553-0.0601-0.00160.17290.08851.0223-37.911959.171449.4333
39-0.11140.39790.35160.7271-0.11211.3251-0.06890.3112-0.9838-0.00510.12950.06720.1394-0.107-0.10530.3042-0.0589-0.02470.2098-0.16361.0778-38.31960.864339.5343
400.4964-0.93320.880.91310.2030.98150.06080.1622-0.732-0.0345-0.09350.10550.06130.03290.02980.3265-0.04270.00480.2785-0.22560.6384-39.659267.521432.174
412.0543-0.0050.49020.61910.25691.0346-0.07490.6904-0.6302-0.02840.0171-0.09880.01-0.14190.03470.2827-0.0282-0.03810.4389-0.11120.3639-41.497677.044929.674
422.5740.6732-0.45441.14760.10960.8568-0.12750.7657-0.1077-0.04180.07880.05160.0193-0.13770.06560.2933-0.0183-0.02890.34890.04640.2854-43.253686.46732.759
432.3745-1.55270.04330.32090.13321.4372-0.14220.07010.28560.02110.06220.1163-0.0689-0.16940.06920.27810.0113-0.01430.18260.05690.283-44.373492.664340.6228
440.2908-0.6022-0.04430.5331-0.24781.4465-0.071-0.35780.17890.01830.0077-0.0146-0.0105-0.14520.03980.30570.0364-0.00880.201-0.01650.3709-44.461493.836550.5957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J
11X-RAY DIFFRACTION11CHAIN K
12X-RAY DIFFRACTION12CHAIN L
13X-RAY DIFFRACTION13CHAIN M
14X-RAY DIFFRACTION14CHAIN N
15X-RAY DIFFRACTION15CHAIN O
16X-RAY DIFFRACTION16CHAIN P
17X-RAY DIFFRACTION17CHAIN Q
18X-RAY DIFFRACTION18CHAIN R
19X-RAY DIFFRACTION19CHAIN S
20X-RAY DIFFRACTION20CHAIN T
21X-RAY DIFFRACTION21CHAIN U
22X-RAY DIFFRACTION22CHAIN V
23X-RAY DIFFRACTION23CHAIN a
24X-RAY DIFFRACTION24CHAIN b
25X-RAY DIFFRACTION25CHAIN c
26X-RAY DIFFRACTION26CHAIN d
27X-RAY DIFFRACTION27CHAIN e
28X-RAY DIFFRACTION28CHAIN f
29X-RAY DIFFRACTION29CHAIN g
30X-RAY DIFFRACTION30CHAIN h
31X-RAY DIFFRACTION31CHAIN i
32X-RAY DIFFRACTION32CHAIN j
33X-RAY DIFFRACTION33CHAIN k
34X-RAY DIFFRACTION34CHAIN l
35X-RAY DIFFRACTION35CHAIN m
36X-RAY DIFFRACTION36CHAIN n
37X-RAY DIFFRACTION37CHAIN o
38X-RAY DIFFRACTION38CHAIN p
39X-RAY DIFFRACTION39CHAIN q
40X-RAY DIFFRACTION40CHAIN r
41X-RAY DIFFRACTION41CHAIN s
42X-RAY DIFFRACTION42CHAIN t
43X-RAY DIFFRACTION43CHAIN u
44X-RAY DIFFRACTION44CHAIN v

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