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- PDB-2v1s: CRYSTAL STRUCTURE OF RAT TOM20-ALDH PRESEQUENCE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2v1s
TitleCRYSTAL STRUCTURE OF RAT TOM20-ALDH PRESEQUENCE COMPLEX
Components
  • ALDEHYDE DEHYDROGENASE
  • MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / MITOCHONDRION / DISULFIDE-BOND TETHERING / STEROID BIOSYNTHESIS / PROTEIN TRANSPORT / STEROL BIOSYNTHESIS / LIPID SYNTHESIS / TRANSIT PEPTIDE / PHOSPHORYLATION / NAD / FAD / MEMBRANE / TRANSPORT / TRANSMEMBRANE / OUTER MEMBRANE / MEMBRANE PROTEIN/OXIDOREDUCTASE
Function / homology
Function and homology information


Ethanol oxidation / cellular response to resveratrol / Metabolism of serotonin / ethanol metabolic process / Mitochondrial protein degradation / tRNA import into mitochondrion / Smooth Muscle Contraction / regulation of response to oxidative stress / PINK1-PRKN Mediated Mitophagy / mitochondrion targeting sequence binding ...Ethanol oxidation / cellular response to resveratrol / Metabolism of serotonin / ethanol metabolic process / Mitochondrial protein degradation / tRNA import into mitochondrion / Smooth Muscle Contraction / regulation of response to oxidative stress / PINK1-PRKN Mediated Mitophagy / mitochondrion targeting sequence binding / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / aldehyde catabolic process / mitochondrial outer membrane translocase complex / phenylacetaldehyde dehydrogenase activity / response to 3,3',5-triiodo-L-thyronine / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / ethanol catabolic process / Ub-specific processing proteases / protein import into mitochondrial matrix / carboxylesterase activity / acetaldehyde metabolic process / NADH binding / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / protein-transporting ATPase activity / aldehyde dehydrogenase (NAD+) / cellular detoxification of aldehyde / behavioral response to ethanol / protein targeting to mitochondrion / aldehyde dehydrogenase (NAD+) activity / mitochondrial envelope / response to muscle activity / regulation of reactive oxygen species metabolic process / cellular response to fatty acid / intrinsic apoptotic signaling pathway in response to oxidative stress / response to testosterone / apoptotic mitochondrial changes / response to hyperoxia / cellular response to hormone stimulus / sperm midpiece / liver development / response to progesterone / cell periphery / response to ischemia / intracellular protein transport / response to nicotine / response to organic cyclic compound / unfolded protein binding / response to estradiol / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / identical protein binding
Similarity search - Function
Mitochondrial outer membrane translocase complex, subunit Tom20 domain / Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / Mitochondrial Import Receptor Subunit Tom20; Chain A / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. ...Mitochondrial outer membrane translocase complex, subunit Tom20 domain / Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / Mitochondrial Import Receptor Subunit Tom20; Chain A / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Aldehyde dehydrogenase, mitochondrial / Mitochondrial import receptor subunit TOM20 homolog
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsObita, T. / Igura, M. / Ose, T. / Endo, T. / Maenaka, K. / Kohda, D.
CitationJournal: Embo J. / Year: 2007
Title: Tom20 Recognizes Mitochondrial Presequences Through Dynamic Equilibrium Among Multiple Bound States.
Authors: Saitoh, T. / Igura, M. / Obita, T. / Ose, T. / Kojima, R. / Maenaka, K. / Endo, T. / Kohda, D.
History
DepositionMay 29, 2007Deposition site: PDBE / Processing site: PDBE
SupersessionJun 12, 2007ID: 2CUV
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 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 / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
B: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
C: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
D: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
E: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
F: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
G: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
H: ALDEHYDE DEHYDROGENASE
I: ALDEHYDE DEHYDROGENASE
J: ALDEHYDE DEHYDROGENASE
K: ALDEHYDE DEHYDROGENASE
L: ALDEHYDE DEHYDROGENASE
M: ALDEHYDE DEHYDROGENASE
N: ALDEHYDE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)65,91114
Polymers65,91114
Non-polymers00
Water6,792377
1
A: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
H: ALDEHYDE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)9,4162
Polymers9,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-8.9 kcal/mol
Surface area6320 Å2
MethodPQS
2
B: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
I: ALDEHYDE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)9,4162
Polymers9,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-9.1 kcal/mol
Surface area6380 Å2
MethodPQS
3
C: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
J: ALDEHYDE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)9,4162
Polymers9,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-8.6 kcal/mol
Surface area6670 Å2
MethodPQS
4
D: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
K: ALDEHYDE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)9,4162
Polymers9,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-8.7 kcal/mol
Surface area6470 Å2
MethodPQS
5
E: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
L: ALDEHYDE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)9,4162
Polymers9,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-8.8 kcal/mol
Surface area6750 Å2
MethodPQS
6
F: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
M: ALDEHYDE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)9,4162
Polymers9,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-9.1 kcal/mol
Surface area5340 Å2
MethodPQS
7
G: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
N: ALDEHYDE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)9,4162
Polymers9,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-7.7 kcal/mol
Surface area2880 Å2
MethodPQS
Unit cell
Length a, b, c (Å)151.781, 64.146, 68.018
Angle α, β, γ (deg.)90.00, 94.70, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.79467, -0.53531, -0.28626), (0.54344, 0.41721, 0.72843), (-0.27051, -0.73442, 0.62245)24.48836, -77.8816, 7.62759
2given(0.49553, -0.59071, -0.63679), (0.6149, -0.27922, 0.73751), (-0.61347, -0.75703, 0.22487)99.09095, -65.22217, 73.17893
3given(-0.33991, 0.34815, 0.87364), (0.3943, -0.79061, 0.46847), (0.85381, 0.50372, 0.13146)77.15728, -29.9652, -45.61061
4given(-0.9522, 0.30428, 0.02709), (0.27893, 0.82985, 0.48326), (0.12456, 0.46772, -0.87506)186.68958, -40.19875, 37.5455
5given(-0.16995, -0.52549, 0.83365), (-0.24268, -0.79759, -0.55223), (0.95511, -0.29616, 0.00803)84.73413, 34.81315, -77.08982
6given(0.68074, 0.58527, -0.44052), (-0.71052, 0.38125, -0.59146), (-0.17821, 0.71562, 0.67537)49.00045, 61.28222, -18.89849
7given(0.80352, -0.54757, -0.23348), (0.49314, 0.39264, 0.77631), (-0.33341, -0.73892, 0.58552)21.7351, -76.22336, 14.77808
8given(0.53488, -0.70864, -0.46015), (0.3776, -0.2867, 0.88046), (-0.75586, -0.64469, 0.11424)90.32259, -50.78632, 88.01978
9given(-0.29939, 0.42838, 0.85256), (0.22141, -0.83796, 0.49879), (0.92809, 0.3381, 0.15603)73.60065, -15.7776, -50.17911
10given(-0.86021, 0.50988, -0.00728), (0.44012, 0.74958, 0.4944), (0.25754, 0.42208, -0.8692)177.08437, -52.5894, 26.58166
11given(-0.46699, -0.21536, 0.85764), (-0.3225, -0.8616, -0.39196), (0.82335, -0.45963, 0.33291)105.29768, 34.64842, -76.41315
12given(-0.49887, 0.27981, 0.82027), (0.5201, -0.66043, 0.5416), (0.69327, 0.69681, 0.18394)97.63625, -74.70602, -74.0444

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Components

#1: Protein
MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG / MITOCHONDRIAL 20 KDA OUTER MEMBRANE PROTEIN / OUTER MITOCHONDRIAL MEMBRANE RECEPTOR TOM20


Mass: 8022.181 Da / Num. of mol.: 7 / Fragment: CYTOSOLIC DOMAIN, RESIDUES 59-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q62760
#2: Protein/peptide
ALDEHYDE DEHYDROGENASE / / ALDH CLASS 2 / ALDH1 / ALDH-E2


Mass: 1393.660 Da / Num. of mol.: 7
Fragment: C-TERMINAL HALF OF THE PRESEQUENCE, RESIDUES 12-24
Mutation: YES / Source method: obtained synthetically / Source: (synth.) RATTUS NORVEGICUS (Norway rat) / References: UniProt: P11884, aldehyde dehydrogenase (NAD+)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN H, ALA 21 TO TYR ENGINEERED RESIDUE IN CHAIN H, ALA 23 TO GLY ...ENGINEERED RESIDUE IN CHAIN H, ALA 21 TO TYR ENGINEERED RESIDUE IN CHAIN H, ALA 23 TO GLY ENGINEERED RESIDUE IN CHAIN H, THR 24 TO CY3 ENGINEERED RESIDUE IN CHAIN I, ALA 21 TO TYR ENGINEERED RESIDUE IN CHAIN I, ALA 23 TO GLY ENGINEERED RESIDUE IN CHAIN I, THR 24 TO CY3 ENGINEERED RESIDUE IN CHAIN J, ALA 21 TO TYR ENGINEERED RESIDUE IN CHAIN J, ALA 23 TO GLY ENGINEERED RESIDUE IN CHAIN J, THR 24 TO CY3 ENGINEERED RESIDUE IN CHAIN K, ALA 21 TO TYR ENGINEERED RESIDUE IN CHAIN K, ALA 23 TO GLY ENGINEERED RESIDUE IN CHAIN K, THR 24 TO CY3 ENGINEERED RESIDUE IN CHAIN L, ALA 21 TO TYR ENGINEERED RESIDUE IN CHAIN L, ALA 23 TO GLY ENGINEERED RESIDUE IN CHAIN L, THR 24 TO CY3 ENGINEERED RESIDUE IN CHAIN M, ALA 21 TO TYR ENGINEERED RESIDUE IN CHAIN M, ALA 23 TO GLY ENGINEERED RESIDUE IN CHAIN M, THR 24 TO CY3 ENGINEERED RESIDUE IN CHAIN N, ALA 21 TO TYR ENGINEERED RESIDUE IN CHAIN N, ALA 23 TO GLY ENGINEERED RESIDUE IN CHAIN N, THR 24 TO CY3
Sequence detailsGLY A 54 CLONING ARTIFACT, PRO A 55 CLONING ARTIFACT, LEU A 56 CLONING ARTIFACT, GLY A 57 CLONING ...GLY A 54 CLONING ARTIFACT, PRO A 55 CLONING ARTIFACT, LEU A 56 CLONING ARTIFACT, GLY A 57 CLONING ARTIFACT, SER A 58 CLONING ARTIFACT, GLY B 54 CLONING ARTIFACT, PRO B 55 CLONING ARTIFACT, LEU B 56 CLONING ARTIFACT, GLY B 57 CLONING ARTIFACT, SER B 58 CLONING ARTIFACT, GLY C 54 CLONING ARTIFACT, PRO C 55 CLONING ARTIFACT, LEU C 56 CLONING ARTIFACT, GLY C 57 CLONING ARTIFACT, SER C 58 CLONING ARTIFACT, GLY D 54 CLONING ARTIFACT, PRO D 55 CLONING ARTIFACT, LEU D 56 CLONING ARTIFACT, GLY D 57 CLONING ARTIFACT, SER D 58 CLONING ARTIFACT, GLY E 54 CLONING ARTIFACT, PRO E 55 CLONING ARTIFACT, LEU E 56 CLONING ARTIFACT, GLY E 57 CLONING ARTIFACT, SER E 58 CLONING ARTIFACT, GLY F 54 CLONING ARTIFACT, PRO F 55 CLONING ARTIFACT, LEU F 56 CLONING ARTIFACT, GLY F 57 CLONING ARTIFACT, SER F 58 CLONING ARTIFACT, GLY G 54 CLONING ARTIFACT, PRO G 55 CLONING ARTIFACT, LEU G 56 CLONING ARTIFACT, GLY G 57 CLONING ARTIFACT, SER G 58 CLONING ARTIFACT

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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 Å3/Da / Density % sol: 59 %
Crystal growMethod: vapor diffusion / pH: 7
Details: PEG6000, AMMONIUM CHROLIDE, HEPES, PH 7.0, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9838
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 4, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9838 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. obs: 34455 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 4.51 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.67
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 1.96 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.47 / % possible all: 64.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OM2

1om2


Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.897 / SU B: 11.861 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.308 3635 9.5 %RANDOM
Rwork0.248 ---
obs0.254 34455 93.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.89 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å22.49 Å2
2--1.83 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 0 377 4232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223913
X-RAY DIFFRACTIONr_bond_other_d0.0010.022640
X-RAY DIFFRACTIONr_angle_refined_deg1.2262.0195265
X-RAY DIFFRACTIONr_angle_other_deg0.9233.0026508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3925473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28426.461178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.0315703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2061512
X-RAY DIFFRACTIONr_chiral_restr0.0690.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024241
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02677
X-RAY DIFFRACTIONr_nbd_refined0.2120.21121
X-RAY DIFFRACTIONr_nbd_other0.1790.22778
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21886
X-RAY DIFFRACTIONr_nbtor_other0.0960.21976
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2284
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1030.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.170.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8441.53196
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93423906
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.49431624
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1424.51359
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
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.295 19
Rwork0.27 1696
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)
13.4365-2.1806-1.32742.37330.6832.1471-0.1143-0.0514-0.01620.01060.03860.01620.1168-0.09470.0757-0.1010.01170.01560.03460.0173-0.06487.37892.422148.4099
26.5135-0.14781.04290.5489-0.18941.0658-0.0509-0.19190.0168-0.022-0.0933-0.12860.0283-0.12660.1442-0.119-0.0168-0.00020.00240.02-0.006778.81465.888612.4981
34.81982.8580.00392.3922-0.32541.10120.14-0.20910.01670.1146-0.08870.1051-0.2255-0.0367-0.05130.0364-0.01390.0646-0.0613-0.0163-0.0987109.417322.901228.7299
44.8468-2.0702-1.26023.89670.13531.45080.2991-0.18810.40440.3429-0.00070.1051-0.212-0.0977-0.29840.04220.04170.1985-0.0060.0222-0.032591.213524.016636.5417
52.34891.08560.27051.63010.24020.83040.0282-0.0097-0.1091-0.0460.0401-0.0187-0.1232-0.0355-0.0682-0.05570.0146-0.0136-0.0061-0.0066-0.0451106.93019.80347.3551
60.6972-0.7924-1.14496.17783.16963.5317-0.3602-0.103-0.24040.620.29780.19230.3043-0.00960.06240.01890.11380.0406-0.04590.0926-0.0737109.2478-14.44246.6826
713.48969.85148.560266.996946.275739.29840.2225-0.188-0.28590.1697-0.3666-3.0808-0.7703-0.77650.1441-0.4948-0.17940.3627-0.22920.14280.054190.4224-24.16829.1341
88.562613.59942.374629.1073-2.07458.71360.8348-0.15570.50070.4587-0.9680.4028-0.59230.08880.1332-0.11890.04440.08760.10080.0549-0.063984.219416.787644.5238
94.5777-0.12176.325210.4968-4.391215.5958-0.31020.4896-0.1204-0.46930.0286-0.2386-0.2452-0.0620.2816-0.124-0.06320.07780.1025-0.0526-0.051170.14435.50040.3083
102.95831.05874.77774.01620.365715.0242-0.04680.1988-0.1757-0.02360.23440.2227-0.5813-0.2434-0.1875-0.03860.01090.0611-0.0173-0.0139-0.0072102.307715.04118.7356
119.9547-0.9023-2.951210.3986-11.516920.87110.2985-0.290.94060.6403-0.29780.1826-0.63910.5551-0.0007-0.04240.00220.1245-0.009-0.0287-0.036892.708211.698740.2892
124.3094-2.22-1.79593.99367.888217.76030.0727-0.06850.3077-0.02060.0576-0.1852-0.3849-0.2086-0.1304-0.0440.02620.0133-0.0517-0.0295-0.0548113.056219.105316.5557
138.9685-10.80038.896313.9346-8.847212.57590.5761-0.72190.0748-0.2005-1.03190.19150.528-1.34260.4559-0.116-0.09950.2390.07310.11090.168399.8135-19.003-1.1361
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A61 - 126
2X-RAY DIFFRACTION2B61 - 126
3X-RAY DIFFRACTION3C58 - 126
4X-RAY DIFFRACTION4D57 - 123
5X-RAY DIFFRACTION5E56 - 126
6X-RAY DIFFRACTION6F63 - 126
7X-RAY DIFFRACTION7G63 - 76
8X-RAY DIFFRACTION8H13 - 24
9X-RAY DIFFRACTION9I14 - 24
10X-RAY DIFFRACTION10J12 - 24
11X-RAY DIFFRACTION11K14 - 24
12X-RAY DIFFRACTION12L12 - 24
13X-RAY DIFFRACTION13M18 - 24

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