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- PDB-2jiz: The Structure of F1-ATPase inhibited by resveratrol. -

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Basic information

Entry
Database: PDB / ID: 2jiz
TitleThe Structure of F1-ATPase inhibited by resveratrol.
Components
  • (ATP SYNTHASE SUBUNIT ...) x 2
  • ATP SYNTHASE GAMMA CHAIN
KeywordsHYDROLASE / MITOCHONDRION / PYRROLIDONE CARBOXYLIC ACID
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / Mitochondrial protein degradation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial inner membrane ...Formation of ATP by chemiosmotic coupling / Cristae formation / Mitochondrial protein degradation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding / plasma membrane
Similarity search - Function
ATP synthase, F1 complex, gamma subunit / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / Pyruvate Kinase; Chain: A, domain 1 / ATP synthase, F1 complex, gamma subunit conserved site ...ATP synthase, F1 complex, gamma subunit / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / Pyruvate Kinase; Chain: A, domain 1 / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / Elongation Factor Tu (Ef-tu); domain 3 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Helix Hairpins / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AZIDE ION / PHOSPHATE ION / RESVERATROL / ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGledhill, J.R. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Mechanism of Inhibition of Bovine F1-ATPase by Resveratrol and Related Polyphenols.
Authors: Gledhill, J.R. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
History
DepositionJul 3, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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_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_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_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_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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 13-STRANDED BARREL THIS IS REPRESENTED BY A 14-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "JA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
B: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
C: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
D: ATP SYNTHASE SUBUNIT BETA
E: ATP SYNTHASE SUBUNIT BETA
F: ATP SYNTHASE SUBUNIT BETA
G: ATP SYNTHASE GAMMA CHAIN
H: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
I: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
J: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
K: ATP SYNTHASE SUBUNIT BETA
L: ATP SYNTHASE SUBUNIT BETA
M: ATP SYNTHASE SUBUNIT BETA
N: ATP SYNTHASE GAMMA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)709,89452
Polymers702,91214
Non-polymers6,98338
Water69,8803879
1
A: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
B: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
C: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
D: ATP SYNTHASE SUBUNIT BETA
E: ATP SYNTHASE SUBUNIT BETA
F: ATP SYNTHASE SUBUNIT BETA
G: ATP SYNTHASE GAMMA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,94726
Polymers351,4567
Non-polymers3,49119
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41180 Å2
ΔGint-211.5 kcal/mol
Surface area103210 Å2
MethodPISA
2
H: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
I: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
J: ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM
K: ATP SYNTHASE SUBUNIT BETA
L: ATP SYNTHASE SUBUNIT BETA
M: ATP SYNTHASE SUBUNIT BETA
N: ATP SYNTHASE GAMMA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,94726
Polymers351,4567
Non-polymers3,49119
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41210 Å2
ΔGint-212 kcal/mol
Surface area103130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.776, 277.368, 137.827
Angle α, β, γ (deg.)90.00, 90.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21H
12B
22I
13C
23J
14D
24K
15E
25L
16F
26M
17G
27N

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A24 - 510
2112H24 - 510
1122B23 - 401
2122I23 - 401
1222B410 - 510
2222I410 - 510
1132C13 - 510
2132J13 - 510
1142D9 - 475
2142K9 - 475
1152E9 - 474
2152L9 - 474
1162F9 - 474
2162M9 - 474
1172G1 - 47
2172N1 - 47
1272G67 - 90
2272N67 - 90
1372G105 - 116
2372N105 - 116
1472G127 - 148
2472N127 - 148
1572G159 - 173
2572N159 - 173
1672G201 - 272
2672N201 - 272

NCS ensembles :
ID
1
2
3
4
5
6
7

NCS oper: (Code: given
Matrix: (1, -2.0E-5, 0.00118), (-1.0E-5, -1, -0.00109), (0.00118, 0.00109, -1)
Vector: -53.47828, 0.06195, 68.98779)

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Components

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ATP SYNTHASE SUBUNIT ... , 2 types, 12 molecules ABCHIJDEFKLM

#1: Protein
ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM / ATP SYNTHASE ALPHA CHAIN HEART ISOFORM


Mass: 55332.219 Da / Num. of mol.: 6 / Fragment: RESIDUES 44-553 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / References: UniProt: P19483, EC: 3.6.1.34
#2: Protein
ATP SYNTHASE SUBUNIT BETA / ATP SYNTHASE BETA CHAIN


Mass: 51757.836 Da / Num. of mol.: 6 / Fragment: RESIDUES 47-528 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / References: UniProt: P00829, EC: 3.6.1.34

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Protein , 1 types, 2 molecules GN

#3: Protein ATP SYNTHASE GAMMA CHAIN


Mass: 30185.674 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-297 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: HEART / References: UniProt: P05631, EC: 3.6.1.34

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Non-polymers , 8 types, 3917 molecules

#4: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#7: 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
#8: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#9: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#10: Chemical ChemComp-STL / RESVERATROL


Mass: 228.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3879 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUE GLN 44 IN UNIPROT SEQUENCE IS MODIFIED TO AN N-TERMINAL PYRROLIDONE CARBOXYLIC ACID RESIDUE ...RESIDUE GLN 44 IN UNIPROT SEQUENCE IS MODIFIED TO AN N-TERMINAL PYRROLIDONE CARBOXYLIC ACID RESIDUE AFTER TRANSIT TO MITOCHONDRION. THIS RESIDUE IS MODELLED HERE AS GLU.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 56.79 % / Description: NONE
Crystal growpH: 8.2 / Details: pH 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→66.82 Å / Num. obs: 299020 / % possible obs: 84.7 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.1 / % possible all: 77.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W0J

1w0j


Resolution: 2.3→138.68 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.737 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 14990 5 %RANDOM
Rwork0.16 ---
obs0.163 284026 84.6 %-
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: 45.17 Å2
Baniso -1Baniso -2Baniso -3
1--2.13 Å20 Å2-0.4 Å2
2--0.86 Å20 Å2
3---1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.3→138.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46464 0 434 3879 50777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02247652
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.99364412
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6256078
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77924.1821956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.643158418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1915348
X-RAY DIFFRACTIONr_chiral_restr0.080.27490
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0235130
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.224010
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.232939
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.24322
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.286
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.289331066
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.149548546
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.737718417
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2231015856
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
11A1948tight positional0.040.1
12H1948tight positional0.040.1
21B1916tight positional0.040.1
22I1916tight positional0.040.1
31C1980tight positional0.040.1
32J1980tight positional0.040.1
41D1868tight positional0.040.1
42K1868tight positional0.040.1
51E1864tight positional0.040.1
52L1864tight positional0.040.1
61F1864tight positional0.040.1
62M1864tight positional0.040.1
71G768tight positional0.040.1
72N768tight positional0.040.1
11A1767medium positional0.170.3
12H1767medium positional0.170.3
21B1742medium positional0.110.3
22I1742medium positional0.110.3
31C1788medium positional0.160.3
32J1788medium positional0.160.3
41D1671medium positional0.150.3
42K1671medium positional0.150.3
51E1666medium positional0.140.3
52L1666medium positional0.140.3
61F1666medium positional0.20.3
62M1666medium positional0.20.3
71G724medium positional0.190.3
72N724medium positional0.190.3
11A1948tight thermal0.865
12H1948tight thermal0.865
21B1916tight thermal0.85
22I1916tight thermal0.85
31C1980tight thermal0.885
32J1980tight thermal0.885
41D1868tight thermal0.895
42K1868tight thermal0.895
51E1864tight thermal0.845
52L1864tight thermal0.845
61F1864tight thermal0.895
62M1864tight thermal0.895
71G768tight thermal1.125
72N768tight thermal1.125
11A1767medium thermal1.7110
12H1767medium thermal1.7110
21B1742medium thermal1.5810
22I1742medium thermal1.5810
31C1788medium thermal1.6910
32J1788medium thermal1.6910
41D1671medium thermal1.6810
42K1671medium thermal1.6810
51E1666medium thermal1.6610
52L1666medium thermal1.6610
61F1666medium thermal1.7310
62M1666medium thermal1.7310
71G724medium thermal1.7910
72N724medium thermal1.7910
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 929
Rwork0.203 17673
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)
13.75850.1386-0.09142.67970.70942.3129-0.06650.416-0.1778-0.12460.0113-0.06720.0885-0.24390.0552-0.0350.01210.0388-0.106-0.0746-0.1346-12.0970.2655-23.2058
20.69080.2634-0.2310.5109-0.24960.5441-0.02380.18640.0241-0.0597-0.0363-0.0173-0.00090.03420.0601-0.0440.03850.00340.02440.0666-0.1511-4.824730.0728-28.8176
31.1744-0.01530.0773.3273-1.10312.61230.08850.05310.1426-0.0039-0.1444-0.1129-0.30810.01940.0559-0.02950.03380.0185-0.08040.157-0.0621-0.752760.8842-30.1252
41.88510.1219-0.03481.69050.17695.33690.06220.1666-0.0357-0.0319-0.0338-0.26840.3060.0018-0.0284-0.05010.09510.0199-0.20270.0708-0.012913.3859-4.18489.5313
50.69530.00610.11160.26630.11740.6998-0.0064-0.010.03180.0286-0.0331-0.0292-0.00730.13510.0395-0.07780.0221-0.0397-0.05770.0992-0.028920.665822.934121.9566
64.3620.82070.08853.71440.47723.18090.1524-0.30660.7345-0.0133-0.0549-0.0061-0.75650.1994-0.09750.0028-0.1277-0.0456-0.16970.0130.00629.548150.368832.4118
72.44820.9475-0.14511.5599-0.25941.06390.0867-0.18540.00720.1869-0.13090.05920.1836-0.05870.04420.0461-0.06160.0065-0.1560.1096-0.0694-28.1565-4.612216.0186
80.4856-0.16260.04790.55440.06350.6356-0.0094-0.06230.01970.0433-0.01240.0467-0.0011-0.11320.0219-0.04750.00150.0203-0.00890.0147-0.0291-35.290426.884617.5562
91.4898-0.6399-0.61381.99040.79461.7862-0.02480.03020.2039-0.0348-0.0437-0.0766-0.2938-0.18010.0685-0.00250.09430.0182-0.099-0.08320.0317-40.034757.189518.6172
101.19890.1939-0.29620.57-0.39722.49-0.05210.1042-0.2464-0.0394-0.03410.06040.3533-0.19840.0862-0.0118-0.0576-0.0079-0.1203-0.0116-0.0723-32.61160.5288-7.431
110.6820.1611-0.3210.3281-0.0220.58130.02060.10360.1183-0.0756-0.01750.0629-0.0585-0.1484-0.0031-0.05130.0348-0.030.01420.0421-0.0502-34.635129.1036-13.8313
121.7084-0.4953-0.53821.19860.37682.16210.1351-0.11890.5525-0.15350.0303-0.0404-0.51040.0324-0.16540.10660.06920.0517-0.09820.04120.1374-28.025558.8982-8.5484
132.67250.59940.84441.2889-1.34663.29230.12420.2415-0.3531-0.0957-0.0974-0.19550.3370.1973-0.0268-0.08820.13630.0562-0.0946-0.0455-0.079110.63040.2796-15.9886
140.72120.13120.08760.5721-0.19170.69410.02660.2166-0.00460.063-0.1054-0.07190.04060.10160.0788-0.19860.04960.0298-0.0110.1286-0.101523.688826.7085-11.8557
152.68880.4519-0.95535.65310.83834.12860.14190.02180.8484-0.0272-0.0843-0.1288-0.91180.3886-0.0576-0.2395-0.1510.0411-0.32590.21640.102132.32256.0205-8.1998
162.6416-0.07970.17810.70960.1111.82520.0568-0.0182-0.28540.0903-0.0782-0.06090.3738-0.01830.02140.05330.0073-0.0093-0.14740.1243-0.0047-3.6994-4.629625.9384
170.8391-0.0760.17290.5271-0.16740.35860.0098-0.22010.04880.0994-0.0358-0.0295-0.0113-0.0390.0260.01540.0089-0.0118-0.01070.0579-0.0705-7.770922.751236.1201
181.22590.5541-0.33631.19040.33971.2428-0.0321-0.19170.39110.17040.0339-0.0866-0.2726-0.0442-0.00180.09160.0139-0.0513-0.1421-0.08440.1017-7.053953.45233.1238
190.9794.77540.267426.82622.33270.37240.0781-0.16330.0932-0.9337-0.28340.2846-0.1074-0.10810.20530.02580.0785-0.0576-0.09650.0104-0.0209-1.095847.89113.3259
202.5461-1.1669-1.041518.28790.53455.03370.3327-0.59170.58371.2046-0.32-0.0323-0.8081-0.2816-0.01270.2036-0.00060.0823-0.6274-0.10310.0008-0.840585.215410.9553
212.68170.0437-0.20751.93360.45542.0644-0.0255-0.26620.20040.24480.01660.0252-0.1467-0.1680.00890.0077-0.0398-0.0096-0.0892-0.0474-0.135441.3255-0.317792.2378
220.7875-0.09820.160.6325-0.20110.46780.0026-0.1951-0.03410.0575-0.0501-0.01020.00240.03260.0475-0.0502-0.0555-0.01650.04490.0836-0.158848.562-30.116597.8638
230.96510.0931-0.14492.8687-0.57992.43960.0158-0.1508-0.250.024-0.0712-0.03760.31870.05620.0555-0.0043-0.0414-0.0253-0.03670.1766-0.058852.5755-60.928499.1861
241.7620.191-0.47021.2079-0.12425.23250.0278-0.17120.0986-0.024-0.0027-0.113-0.31980.1594-0.0251-0.0422-0.11380.001-0.19390.09570.00266.76184.158159.5657
250.57970.0561-0.25650.40440.15860.7734-0.00440.0317-0.0533-0.0217-0.024-0.05830.01490.11030.0284-0.096-0.02030.0275-0.05560.1114-0.030874.0576-22.928147.1062
263.8802-0.966-0.50264.18940.33912.83320.12180.3248-0.60310.03720.00370.00980.73510.2407-0.1255-0.03040.12390.0377-0.14270.0259-0.017382.9499-50.343436.6064
271.4713-0.8322-0.21372.6323-0.04780.84020.12120.1480.0041-0.2036-0.1190.0996-0.1430.0248-0.00210.03410.0601-0.0025-0.13370.0916-0.101825.21144.616753.0039
280.59660.1879-0.10080.41250.10370.7790.01880.08560.0027-0.0153-0.02330.0363-0.0034-0.09790.0045-0.0488-0.002-0.0257-0.01970.0254-0.037118.1144-26.874151.3961
291.31570.26310.7481.76510.51371.801-0.0711-0.0136-0.2542-0.0418-0.016-0.04150.2581-0.13550.0871-0.0218-0.0951-0.0106-0.0879-0.06270.039713.4398-57.167750.2899
301.6057-0.79640.61050.7422-0.01833.1915-0.0471-0.09940.24910.03330.06770.1525-0.3471-0.2054-0.0206-0.03010.0430.0273-0.1203-0.002-0.067420.7757-0.550176.4343
310.7558-0.10130.32280.3598-0.03190.63610.0166-0.0966-0.12510.0516-0.01660.05140.0553-0.14190-0.0606-0.03770.0240.01240.051-0.060418.758-29.123782.7968
320.99420.62370.31841.29040.56182.05010.1685-0.0269-0.53490.16890.02930.01210.59210.0124-0.19780.1246-0.0632-0.0414-0.10510.06620.165425.3762-58.904277.5148
332.9778-0.7478-0.52140.5619-0.10822.09370.116-0.24420.35390.1126-0.0724-0.2157-0.26490.1778-0.0436-0.0644-0.1316-0.0557-0.0806-0.0301-0.087664.0222-0.32285.0894
340.8297-0.1389-0.13890.6877-0.17450.63870.0291-0.21880.0051-0.0457-0.1248-0.0642-0.0760.1120.0957-0.2079-0.0695-0.03470.00170.1469-0.114377.0815-26.744580.9649
351.9407-0.07840.87995.45211.09314.22240.1248-0.179-0.89350.0003-0.1701-0.19270.95170.39890.0453-0.22980.1261-0.0137-0.31230.2380.107785.7011-56.051677.2697
362.71780.6312-0.85951.32780.28340.73280.04350.08670.2951-0.0583-0.0405-0.0073-0.2849-0.0245-0.00290.0520.0030.0132-0.1630.1421-0.010149.6844.636643.1083
370.9130.0227-0.06820.483-0.15370.29160.02360.2029-0.0405-0.0804-0.0351-0.0059-0.0003-0.02640.01160.0065-0.01180.0108-0.02510.0593-0.071845.6185-22.718632.8859
381.2958-0.10520.23031.20580.01630.859-0.02890.2069-0.3777-0.12480.0749-0.06250.2508-0.0313-0.0460.07110.00760.0514-0.1365-0.08770.064346.3534-53.442435.8428
390.9357-4.0648-0.186321.71712.11460.45680.03330.0955-0.11471.0021-0.27910.41690.1439-0.10860.24580.057-0.10.0691-0.11060.04180.006752.2908-47.892465.7089
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 95
2X-RAY DIFFRACTION2A96 - 379
3X-RAY DIFFRACTION2A600 - 700
4X-RAY DIFFRACTION3A380 - 510
5X-RAY DIFFRACTION4B23 - 95
6X-RAY DIFFRACTION5B96 - 379
7X-RAY DIFFRACTION5B600 - 700
8X-RAY DIFFRACTION6B380 - 510
9X-RAY DIFFRACTION7C13 - 95
10X-RAY DIFFRACTION8C96 - 379
11X-RAY DIFFRACTION8C600 - 700
12X-RAY DIFFRACTION9C380 - 510
13X-RAY DIFFRACTION10D9 - 82
14X-RAY DIFFRACTION11D83 - 363
15X-RAY DIFFRACTION11D600 - 700
16X-RAY DIFFRACTION12D364 - 475
17X-RAY DIFFRACTION13E9 - 82
18X-RAY DIFFRACTION14E83 - 363
19X-RAY DIFFRACTION14E602
20X-RAY DIFFRACTION15E364 - 474
21X-RAY DIFFRACTION16F9 - 82
22X-RAY DIFFRACTION17F83 - 363
23X-RAY DIFFRACTION17F600 - 700
24X-RAY DIFFRACTION18F364 - 474
25X-RAY DIFFRACTION19G1 - 30
26X-RAY DIFFRACTION19G220 - 272
27X-RAY DIFFRACTION20G31 - 219
28X-RAY DIFFRACTION21H24 - 95
29X-RAY DIFFRACTION22H96 - 379
30X-RAY DIFFRACTION22H600 - 700
31X-RAY DIFFRACTION23H380 - 510
32X-RAY DIFFRACTION24I23 - 95
33X-RAY DIFFRACTION25I96 - 379
34X-RAY DIFFRACTION25I600 - 700
35X-RAY DIFFRACTION26I380 - 510
36X-RAY DIFFRACTION27J13 - 95
37X-RAY DIFFRACTION28J96 - 379
38X-RAY DIFFRACTION28J600 - 700
39X-RAY DIFFRACTION29J380 - 510
40X-RAY DIFFRACTION30K9 - 82
41X-RAY DIFFRACTION31K83 - 363
42X-RAY DIFFRACTION31K600 - 700
43X-RAY DIFFRACTION32K364 - 475
44X-RAY DIFFRACTION33L9 - 82
45X-RAY DIFFRACTION34L83 - 363
46X-RAY DIFFRACTION34L602
47X-RAY DIFFRACTION35L364 - 474
48X-RAY DIFFRACTION36M9 - 82
49X-RAY DIFFRACTION37M83 - 363
50X-RAY DIFFRACTION37M600 - 700
51X-RAY DIFFRACTION38M364 - 474
52X-RAY DIFFRACTION39N1 - 30
53X-RAY DIFFRACTION39N220 - 272

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