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- PDB-2hld: Crystal structure of yeast mitochondrial F1-ATPase -

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Basic information

Entry
Database: PDB / ID: 2hld
TitleCrystal structure of yeast mitochondrial F1-ATPase
Components(ATP synthase ...) x 5
KeywordsHYDROLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / ATP SYNTHASE / F1FO / F1-ATPASE
Function / homology
Function and homology information


: / Mitochondrial protein degradation / : / : / : / mitochondrial nucleoid / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase ...: / Mitochondrial protein degradation / : / : / : / mitochondrial nucleoid / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial intermembrane space / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding / cytosol
Similarity search - Function
Helix Hairpins - #880 / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / Atp Synthase Epsilon Chain; Chain: I; / : / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / ATP synthase alpha/beta chain, C-terminal domain / Lysin ...Helix Hairpins - #880 / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / Atp Synthase Epsilon Chain; Chain: I; / : / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Pyruvate Kinase; Chain: A, domain 1 / 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 / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / Helix Hairpins / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / 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, 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, F1 complex, alpha subunit nucleotide-binding domain / 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 non-globular / Special / 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 / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHATE ION / ATP synthase subunit beta, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit delta, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKabaleeswaran, V. / Puri, N. / Walker, J.E. / Leslie, A.G. / Mueller, D.M.
Citation
Journal: Embo J. / Year: 2006
Title: Novel features of the rotary catalytic mechanism revealed in the structure of yeast F(1) ATPase.
Authors: Kabaleeswaran, V. / Puri, N. / Walker, J.E. / Leslie, A.G. / Mueller, D.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and preliminary crystallographic studies of the mitochondrial F1-ATPase from the yeast Saccharomyces cerevisiae.
Authors: Mueller, D.M. / Puri, N. / Kabaleeswaran, V. / Terry, C. / Leslie, A.G. / Walker, J.E.
#2: Journal: Embo J. / Year: 2004
Title: The structure of bovine F1-ATPase inhibited by ADP and beryllium fluoride.
Authors: Kagawa, R. / Montgomery, M.G. / Braig, K. / Leslie, A.G. / Walker, J.E.
#3: Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structure of bovine mitochondrial F(1)-ATPase with nucleotide bound to all three catalytic sites: implications for the mechanism of rotary catalysis.
Authors: Menz, R.I. / Walker, J.E. / Leslie, A.G.
#4: Journal: Nat.Struct.Mol.Biol. / Year: 2000
Title: The structure of the central stalk in bovine F1-ATPase at 2.4 A resolution
Authors: Gibbons, C. / Montgomery, M.G. / Leslie, A.G. / Walker, J.E.
#5: Journal: Science / Year: 1999
Title: Molecular architecture of the rotary motor in ATP synthase.
Authors: Stock, D. / Leslie, A.G. / Walker, J.E.
#6: Journal: Nature / Year: 1994
Title: Structure at 2.8 A resolution of F1-ATPase from bovine heart mitochondria
Authors: Abrahams, J.P. / Leslie, A.G. / Lutter, R. / Walker, J.E.
History
DepositionJul 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Aug 30, 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 / pdbx_struct_conn_angle / 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 / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 400 COMPOUND THE F1-ATPASE MOLECULE HAS THREE COPIES OF THE ALPHA SUBUNIT AND THREE COPIES OF THE BETA ... COMPOUND THE F1-ATPASE MOLECULE HAS THREE COPIES OF THE ALPHA SUBUNIT AND THREE COPIES OF THE BETA SUBUNIT. THERE ARE THREE COPIES OF THE F1 ATPASE IN THE ASYMMETRIC UNIT FORMED BY CHAINS A-I (COPY 1), J-R (COPY 2), AND S-1 (COPY 3). THERE ARE THREE CATALYTIC AND THREE NONCATALYTIC NUCLEOTIDE BINDING SITES FORMED BY THE ALPHA AND BETA SUBUNITS. THE ALPHA AND BETA SUBUNITS ARE NAMED AS RELATING TO THE CORRESPONDING SUBUNITS FORMING THE ACTIVE SITES, AS IN REFERENCE 6, BETA (DP), BETA (E), AND BETA (TP). THE CORRESPONDENCE BETWEEN THE SUBUNIT NAMES AND THE CHAIN IDENTIFIERS IS GIVEN BELOW: CHAIN A, J, S: ALPHA SUBUNIT(E) CHAIN B, K, T: ALPHA SUBUNIT (TP) CHAIN C, L, U: ALPHA SUBUNIT (DP) CHAIN D, M, V: BETA SUBUNIT (DP) CHAIN E, N, W: BETA SUBUNIT (E) CHAIN F, O, X: BETA SUBUNIT (TP) CHAIN G, P, Y: GAMMA SUBUNIT CHAIN H, Q, Z: DELTA SUBUNIT CHAIN I, R, 1: EPSILON SUBUNIT IN YEAST F1-ATPASE THE CATALYTIC DP AND TP SITES ARE OCCUPIED WITH AMP/PNP AND CHAIN N HAS PHOSPHATE BOUND.
Remark 999SEQUENCE THE RESIDUE NUMBERING IN THE COORDINATES IS WITH RESPECT TO THE MATURE PEPTIDE. THE ...SEQUENCE THE RESIDUE NUMBERING IN THE COORDINATES IS WITH RESPECT TO THE MATURE PEPTIDE. THE NUMBERING IN THE SEQUENCE DATABASE IS UNPROCESSED PRECURSOR NUMBERING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP synthase alpha chain, mitochondrial
B: ATP synthase alpha chain, mitochondrial
C: ATP synthase alpha chain, mitochondrial
D: ATP synthase beta chain, mitochondrial
E: ATP synthase beta chain, mitochondrial
F: ATP synthase beta chain, mitochondrial
G: ATP synthase gamma chain, mitochondrial
H: ATP synthase delta chain, mitochondrial
I: ATP synthase epsilon chain, mitochondrial
J: ATP synthase alpha chain, mitochondrial
K: ATP synthase alpha chain, mitochondrial
L: ATP synthase alpha chain, mitochondrial
M: ATP synthase beta chain, mitochondrial
N: ATP synthase beta chain, mitochondrial
O: ATP synthase beta chain, mitochondrial
P: ATP synthase gamma chain, mitochondrial
Q: ATP synthase delta chain, mitochondrial
R: ATP synthase epsilon chain, mitochondrial
S: ATP synthase alpha chain, mitochondrial
T: ATP synthase alpha chain, mitochondrial
U: ATP synthase alpha chain, mitochondrial
V: ATP synthase beta chain, mitochondrial
W: ATP synthase beta chain, mitochondrial
X: ATP synthase beta chain, mitochondrial
Y: ATP synthase gamma chain, mitochondrial
Z: ATP synthase delta chain, mitochondrial
1: ATP synthase epsilon chain, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,119,27258
Polymers1,111,21927
Non-polymers8,05231
Water3,297183
1
A: ATP synthase alpha chain, mitochondrial
B: ATP synthase alpha chain, mitochondrial
C: ATP synthase alpha chain, mitochondrial
D: ATP synthase beta chain, mitochondrial
E: ATP synthase beta chain, mitochondrial
F: ATP synthase beta chain, mitochondrial
G: ATP synthase gamma chain, mitochondrial
H: ATP synthase delta chain, mitochondrial
I: ATP synthase epsilon chain, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,05919
Polymers370,4069
Non-polymers2,65310
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40560 Å2
ΔGint-200 kcal/mol
Surface area118140 Å2
MethodPISA
2
J: ATP synthase alpha chain, mitochondrial
K: ATP synthase alpha chain, mitochondrial
L: ATP synthase alpha chain, mitochondrial
M: ATP synthase beta chain, mitochondrial
N: ATP synthase beta chain, mitochondrial
O: ATP synthase beta chain, mitochondrial
P: ATP synthase gamma chain, mitochondrial
Q: ATP synthase delta chain, mitochondrial
R: ATP synthase epsilon chain, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,15420
Polymers370,4069
Non-polymers2,74711
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40490 Å2
ΔGint-203 kcal/mol
Surface area115780 Å2
MethodPISA
3
S: ATP synthase alpha chain, mitochondrial
T: ATP synthase alpha chain, mitochondrial
U: ATP synthase alpha chain, mitochondrial
V: ATP synthase beta chain, mitochondrial
W: ATP synthase beta chain, mitochondrial
X: ATP synthase beta chain, mitochondrial
Y: ATP synthase gamma chain, mitochondrial
Z: ATP synthase delta chain, mitochondrial
1: ATP synthase epsilon chain, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,05919
Polymers370,4069
Non-polymers2,65310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.524, 294.132, 190.432
Angle α, β, γ (deg.)90.00, 101.67, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21J
31S
12B
22K
32T
13C
23L
33U
43C
53L
63U
14D
24M
34V
15E
25N
35W
16F
26O
36X

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNVALVALAA26 - 50726 - 507
211ASNASNVALVALJJ26 - 50726 - 507
311LEULEUVALVALSS27 - 50727 - 507
112ALAALAVALVALBB25 - 50725 - 507
212GLUGLUVALVALKK24 - 50724 - 507
312ASNASNVALVALTT26 - 50726 - 507
113ASNASNALAALACC26 - 38026 - 380
213ASNASNALAALALL26 - 38026 - 380
313ASNASNALAALAUU26 - 38026 - 380
423LEULEUVALVALCC420 - 507420 - 507
523LEULEUVALVALLL420 - 507420 - 507
623LEULEUVALVALUU420 - 507420 - 507
114THRTHRALAALADD10 - 47410 - 474
214THRTHRALAALAMM10 - 47410 - 474
314THRTHRALAALAVV10 - 47410 - 474
115THRTHRALAALAEE10 - 47410 - 474
215THRTHRALAALANN10 - 47410 - 474
315THRTHRALAALAWW10 - 47410 - 474
116THRTHRALAALAFF10 - 47410 - 474
216THRTHRALAALAOO10 - 47410 - 474
316THRTHRALAALAXX10 - 47410 - 474

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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ATP synthase ... , 5 types, 27 molecules ABCJKLSTUDEFMNOVWXGPYHQZIR1

#1: Protein
ATP synthase alpha chain, mitochondrial


Mass: 55007.402 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Organelle: MITOCHONDRIA
References: UniProt: P07251, H+-transporting two-sector ATPase
#2: Protein
ATP synthase beta chain, mitochondrial


Mass: 51181.082 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATP2 / Organelle: MITOCHONDRIA / Plasmid: pRS314 / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00830, H+-transporting two-sector ATPase
#3: Protein ATP synthase gamma chain, mitochondrial


Mass: 30657.160 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Organelle: MITOCHONDRIA
References: UniProt: P38077, H+-transporting two-sector ATPase
#4: Protein ATP synthase delta chain, mitochondrial


Mass: 14565.385 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Organelle: MITOCHONDRIA
References: UniProt: Q12165, H+-transporting two-sector ATPase
#5: Protein ATP synthase epsilon chain, mitochondrial


Mass: 6618.359 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Organelle: MITOCHONDRIA
References: UniProt: P21306, H+-transporting two-sector ATPase

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Non-polymers , 4 types, 214 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 5.5% PEG 6000, 10% glycerol, 4% methanol, 0.05M sodium acetate, 0.5mM nickel sulphate, 0.5mM AMP/PNP, 0.025 mM ADP, 2mM magnesium chloride, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 9, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 346124 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.7
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.6 / Num. unique all: 36073 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E1Q

1e1q


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 27.512 / SU ML: 0.289 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24412 5938 2 %RANDOM
Rwork0.20659 ---
obs0.20731 286907 99.94 %-
all-293909 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 70.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å2-0.91 Å2
2---0.42 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms72173 0 485 183 72841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02273739
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.97599993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62659540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25724.4892983
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0831512613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.68915482
X-RAY DIFFRACTIONr_chiral_restr0.0860.211757
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0254644
X-RAY DIFFRACTIONr_nbd_refined0.2160.232300
X-RAY DIFFRACTIONr_nbtor_refined0.3070.250577
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.22425
X-RAY DIFFRACTIONr_metal_ion_refined0.1390.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.26
X-RAY DIFFRACTIONr_mcbond_it1.645348649
X-RAY DIFFRACTIONr_mcangle_it2.828576094
X-RAY DIFFRACTIONr_scbond_it4.401727633
X-RAY DIFFRACTIONr_scangle_it6.4621023899
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3630tight positional0.150.1
12J3630tight positional0.160.1
13S3630tight positional0.130.1
21B3647tight positional0.10.1
22K3647tight positional0.110.1
23T3647tight positional0.10.1
31C3370tight positional0.150.1
32L3370tight positional0.170.1
33U3370tight positional0.10.1
41D3516tight positional0.150.1
42M3516tight positional0.190.1
43V3516tight positional0.120.1
51E3516tight positional0.10.1
52N3516tight positional0.120.1
53W3516tight positional0.090.1
61F3516tight positional0.110.1
62O3516tight positional0.110.1
63X3516tight positional0.10.1
11A3630tight thermal6.3510
12J3630tight thermal5.0210
13S3630tight thermal6.9410
21B3647tight thermal4.1410
22K3647tight thermal3.8610
23T3647tight thermal4.7610
31C3370tight thermal5.5510
32L3370tight thermal6.2910
33U3370tight thermal8.8210
41D3516tight thermal5.4510
42M3516tight thermal5.6810
43V3516tight thermal8.710
51E3516tight thermal3.7410
52N3516tight thermal3.2910
53W3516tight thermal3.7710
61F3516tight thermal4.5510
62O3516tight thermal4.5810
63X3516tight thermal4.8310
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 452 -
Rwork0.348 20697 -
obs--99.58 %
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)
12.798-0.3916-0.43751.258-0.00961.4562-0.12020.0421-0.0894-0.01180.10180.24820.0174-0.28570.0184-0.4498-0.0104-0.0647-0.4648-0.0687-0.5391-10.08855.03166.5894
21.56730.42570.25851.98690.33642.3821-0.13950.2291-0.3219-0.69070.1060.0010.3421-0.14470.0335-0.16330.0077-0.0425-0.7383-0.1033-0.353117.2652-29.911328.7231
31.7236-0.1950.27282.2859-0.26492.05090.00060.20630.5053-0.56660.1-0.2712-0.3690.0387-0.1005-0.2232-0.08450.0927-0.6533-0.0289-0.237630.630525.744633.3446
41.52190.3003-0.20511.6461-0.09993.6696-0.04940.3538-0.0679-0.5343-0.0128-0.2953-0.11920.25160.0622-0.1537-0.08190.0975-0.3584-0.0432-0.422817.0238-100.859442.9866
52.45120.1674-0.19692.1158-0.26981.71090.32910.19720.74360.0333-0.070.7656-1.0649-0.3441-0.25910.37730.12880.181-0.558-0.1265-0.0075-17.1207-67.050575.8932
61.43130.5477-0.36232.175-0.38232.3312-0.0774-0.0115-0.2331-0.1749-0.0070.17220.2152-0.25170.0844-0.4667-0.094-0.0149-0.4717-0.0468-0.5244-15.1318-123.851983.0697
72.86361.2765-0.60793.6728-0.47072.42010.2822-0.13590.23740.1395-0.1087-0.05010.2709-0.4671-0.17350.1919-0.1668-0.2728-0.4688-0.0927-0.411951.4856-20.3521161.3029
82.36650.20790.41732.39980.15412.97340.03060.30790.3271-0.1999-0.21940.57470.0959-0.93870.18870.1501-0.25-0.12860.561-0.29180.03683.1684-33.5386130.5058
92.2714-0.33620.81042.63050.44612.77030.281-0.2695-0.66150.3443-0.0899-0.62940.8554-0.0814-0.19111.1173-0.5654-0.4572-0.68520.07680.168741.3609-73.4397145.4313
103.6046-0.47460.51881.9614-0.34741.6223-0.0699-0.0770.663-0.11320.2063-0.0218-0.4353-0.0918-0.1364-0.3765-0.0211-0.0255-0.6112-0.1293-0.324810.305128.885156.3384
111.58390.6678-0.00372.0502-0.06442.9348-0.07040.0574-0.3588-0.28790.02480.05610.34770.21030.0456-0.34840.0060.0385-0.53950.0161-0.32055.3799-125.477961.9287
123.80720.4596-0.39752.4271-0.30594.20340.3426-0.1664-0.68840.1719-0.1009-0.56291.12170.1928-0.24170.7944-0.196-0.5598-0.7212-0.0047-0.085658.0336-52.6659160.8703
133.56650.84350.28982.23951.1182.1844-0.00770.0264-0.4787-0.0757-0.17690.59740.3111-0.72520.1846-0.3851-0.0331-0.067-0.47740.029-0.2303-6.5366-25.889353.7581
142.02350.0165-0.74262.4613-1.25183.04780.21980.61490.5052-0.46860.06860.1861-0.5744-0.365-0.28840.159-0.11150.0388-0.32930.0594-0.31716.7294-70.605750.0939
152.0890.49160.23433.1996-0.88862.362-0.05330.08630.6418-0.0732-0.08620.0673-0.0944-0.43660.13940.07-0.12060.01310.2075-0.24780.012122.9089-9.4524146.33
161.6929-0.18280.27831.6411-0.42262.30910.04740.46810.0146-0.6845-0.0098-0.48420.1090.2919-0.0376-0.15590.01840.1545-0.5497-0.0733-0.367234.0762-5.087121.9889
172.26280.3216-0.13491.524-0.1462.07730.3034-0.26170.30860.2894-0.13240.6159-0.594-0.58-0.1711-0.1205-0.00390.083-0.3497-0.1979-0.3316-24.5733-92.873590.2904
181.2771-0.0275-0.23381.97490.26073.02480.0447-0.2131-0.32440.1936-0.19770.31940.5562-0.98760.1530.3199-0.7502-0.16970.1929-0.1588-0.079813.1361-62.2834132.5437
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 90
2X-RAY DIFFRACTION1A95 - 378
3X-RAY DIFFRACTION1A380 - 507
4X-RAY DIFFRACTION2B30 - 90
5X-RAY DIFFRACTION2B95 - 378
6X-RAY DIFFRACTION2B380 - 507
7X-RAY DIFFRACTION3C30 - 90
8X-RAY DIFFRACTION3C95 - 378
9X-RAY DIFFRACTION3C380 - 507
10X-RAY DIFFRACTION4J30 - 90
11X-RAY DIFFRACTION4J95 - 378
12X-RAY DIFFRACTION4J380 - 507
13X-RAY DIFFRACTION5K30 - 90
14X-RAY DIFFRACTION5K95 - 378
15X-RAY DIFFRACTION5K380 - 507
16X-RAY DIFFRACTION6L30 - 90
17X-RAY DIFFRACTION6L95 - 378
18X-RAY DIFFRACTION6L380 - 507
19X-RAY DIFFRACTION7S30 - 90
20X-RAY DIFFRACTION7S95 - 378
21X-RAY DIFFRACTION7S380 - 507
22X-RAY DIFFRACTION8T30 - 90
23X-RAY DIFFRACTION8T95 - 378
24X-RAY DIFFRACTION8T380 - 507
25X-RAY DIFFRACTION9U30 - 90
26X-RAY DIFFRACTION9U95 - 378
27X-RAY DIFFRACTION9U380 - 507
28X-RAY DIFFRACTION10D14 - 78
29X-RAY DIFFRACTION10D85 - 357
30X-RAY DIFFRACTION10D360 - 474
31X-RAY DIFFRACTION11M14 - 78
32X-RAY DIFFRACTION11M85 - 357
33X-RAY DIFFRACTION11M360 - 474
34X-RAY DIFFRACTION12V14 - 78
35X-RAY DIFFRACTION12V85 - 357
36X-RAY DIFFRACTION12V360 - 474
37X-RAY DIFFRACTION13E14 - 78
38X-RAY DIFFRACTION13E85 - 357
39X-RAY DIFFRACTION13E360 - 474
40X-RAY DIFFRACTION14N14 - 78
41X-RAY DIFFRACTION14N85 - 357
42X-RAY DIFFRACTION14N360 - 474
43X-RAY DIFFRACTION15W14 - 78
44X-RAY DIFFRACTION15W85 - 357
45X-RAY DIFFRACTION15W360 - 474
46X-RAY DIFFRACTION16F14 - 78
47X-RAY DIFFRACTION16F85 - 357
48X-RAY DIFFRACTION16F360 - 474
49X-RAY DIFFRACTION17O14 - 78
50X-RAY DIFFRACTION17O85 - 357
51X-RAY DIFFRACTION17O360 - 474
52X-RAY DIFFRACTION18X14 - 78
53X-RAY DIFFRACTION18X85 - 357
54X-RAY DIFFRACTION18X360 - 474

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