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- PDB-2wp9: Crystal structure of the E. coli succinate:quinone oxidoreductase... -

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Basic information

Entry
Database: PDB / ID: 2wp9
TitleCrystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhB His207Thr mutant
Components(SUCCINATE DEHYDROGENASE ...) x 4
KeywordsOXIDOREDUCTASE / CELL INNER MEMBRANE / TRICARBOXYLIC ACID CYCLE / METAL-BINDING / TRANSMEMBRANE / FLAVOPROTEIN / ELECTRON TRANSPORT
Function / homology
Function and homology information


: / : / succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / cytochrome complex assembly / aerobic electron transport chain / anaerobic respiration / 3 iron, 4 sulfur cluster binding / ubiquinone binding ...: / : / succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / cytochrome complex assembly / aerobic electron transport chain / anaerobic respiration / 3 iron, 4 sulfur cluster binding / ubiquinone binding / iron-sulfur cluster binding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Succinate dehydrogenase, hydrophobic membrane anchor / succinate dehydrogenase protein domain / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit ...Succinate dehydrogenase, hydrophobic membrane anchor / succinate dehydrogenase protein domain / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 3 helical TM bundles of succinate and fumarate reductases / 4Fe-4S dicluster domain / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / Alpha-helical ferredoxin / FAD binding domain / Rhinovirus 14, subunit 4 / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 3-Layer(bba) Sandwich / Ubiquitin-like (UB roll) / FAD/NAD(P)-binding domain superfamily / Few Secondary Structures / Irregular / Roll / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-CBE / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / IRON/SULFUR CLUSTER / MALATE LIKE INTERMEDIATE / Succinate dehydrogenase iron-sulfur subunit / Succinate dehydrogenase flavoprotein subunit / Succinate dehydrogenase hydrophobic membrane anchor subunit / Succinate dehydrogenase cytochrome b556 subunit
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRuprecht, J. / Yankovskaya, V. / Maklashina, E. / Iwata, S. / Cecchini, G.
CitationJournal: J. Biol. Chem. / Year: 2011
Title: Perturbation of the quinone-binding site of complex II alters the electronic properties of the proximal [3Fe-4S] iron-sulfur cluster.
Authors: Ruprecht, J. / Iwata, S. / Rothery, R.A. / Weiner, J.H. / Maklashina, E. / Cecchini, G.
History
DepositionAug 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection / Database references / Category: atom_site / citation
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 2.1Dec 20, 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_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_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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET 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: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
B: SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
C: SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT
D: SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT
E: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
F: SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
G: SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT
H: SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT
I: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
J: SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
K: SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT
L: SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,20936
Polymers355,36312
Non-polymers7,84724
Water2,306128
1
A: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
B: SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
C: SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT
D: SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,07012
Polymers118,4544
Non-polymers2,6168
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15530 Å2
ΔGint-158.3 kcal/mol
Surface area38170 Å2
MethodPISA
2
E: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
F: SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
G: SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT
H: SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,07012
Polymers118,4544
Non-polymers2,6168
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15560 Å2
ΔGint-158.9 kcal/mol
Surface area38220 Å2
MethodPISA
3
I: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
J: SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
K: SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT
L: SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,07012
Polymers118,4544
Non-polymers2,6168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15520 Å2
ΔGint-160.1 kcal/mol
Surface area38230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.853, 183.803, 202.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
31I
12B
22F
32J
13C
23G
33K
14D
24H
34L

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTYRTYRAA1 - 5881 - 588
21METMETTYRTYREE1 - 5881 - 588
31METMETTYRTYRII1 - 5881 - 588
12METMETALAALABB1 - 2381 - 238
22METMETALAALAFF1 - 2381 - 238
32METMETALAALAJJ1 - 2381 - 238
13GLNGLNTRPTRPCC8 - 1298 - 129
23GLNGLNTRPTRPGG8 - 1298 - 129
33GLNGLNTRPTRPKK8 - 1298 - 129
14ASNASNVALVALDD11 - 11511 - 115
24ASNASNVALVALHH11 - 11511 - 115
34ASNASNVALVALLL11 - 11511 - 115

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.94922, 0.28667, 0.12962), (0.25688, -0.46833, -0.84539), (-0.18164, 0.83576, -0.51818)17.3606, -98.5621, -29.69555
2given(0.95038, 0.26894, -0.15639), (0.26932, -0.4596, 0.84631), (0.15573, -0.84643, -0.50922)3.6848, -25.04748, -101.99783
3given(0.95136, 0.28208, 0.12384), (0.24987, -0.47139, -0.84579), (-0.1802, 0.8356, -0.51894)17.14904, -98.45415, -29.81741
4given(0.95009, 0.26014, -0.17221), (0.27882, -0.46037, 0.84281), (0.13997, -0.84876, -0.50992)3.17224, -25.39694, -101.67189
5given(0.95075, 0.28367, 0.12494), (0.25014, -0.46413, -0.84971), (-0.18305, 0.83911, -0.51223)17.34645, -98.44913, -29.51782
6given(0.94862, 0.25726, -0.18424), (0.28814, -0.46161, 0.83899), (0.13079, -0.84896, -0.51201)2.89664, -25.73201, -101.30891
7given(0.95176, 0.28127, 0.12264), (0.24533, -0.45746, -0.85471), (-0.1843, 0.84357, -0.5044)17.1711, -98.2444, -29.04328
8given(0.94825, 0.25616, -0.18764), (0.28928, -0.4532, 0.84317), (0.13095, -0.85381, -0.50384)2.78004, -25.55106, -101.16541

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Components

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SUCCINATE DEHYDROGENASE ... , 4 types, 12 molecules AEIBFJCGKDHL

#1: Protein SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT


Mass: 64502.766 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: FAD ATOM C8M IS COVALENTLY LINKED TO NE2 OF SDHA HIS45
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PFAS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DW35
References: UniProt: P0AC41, succinate dehydrogenase, succinate dehydrogenase
#2: Protein SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT


Mass: 26763.869 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PFAS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DW35
References: UniProt: P07014, succinate dehydrogenase, succinate dehydrogenase
#3: Protein SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT / SUCCINATE DEHYDROGENASE CYTOCHROME B-556 SUBUNIT / CYTOCHROME B-556


Mass: 14313.100 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: RESIDUES 8-129 MODELLED / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PFAS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DW35 / References: UniProt: P69054, succinate dehydrogenase
#4: Protein SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT / SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN


Mass: 12874.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: RESIDUES 11-115 MODELLED / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PFAS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DW35 / References: UniProt: P0AC44, succinate dehydrogenase

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Non-polymers , 9 types, 152 molecules

#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical ChemComp-TEO / MALATE LIKE INTERMEDIATE


Mass: 132.072 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H4O5
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2
#9: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe3S4
#11: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#12: Chemical ChemComp-CBE / 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE / 5,6-DIHYDRO-2-METHYL-1,4-OXATHIIN-3-CARBOXANILID / CARBOXIN / CBX


Mass: 235.302 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H13NO2S
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN B, HIS 207 TO THR ENGINEERED RESIDUE IN CHAIN F, HIS 207 TO THR ...ENGINEERED RESIDUE IN CHAIN B, HIS 207 TO THR ENGINEERED RESIDUE IN CHAIN F, HIS 207 TO THR ENGINEERED RESIDUE IN CHAIN J, HIS 207 TO THR

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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: 3.1 Å3/Da / Density % sol: 60.37 %
Description: PHASES INITIALLY DETERMINED BY RIGID-BODY REFINEMENT OF 2WDQ AGAINST THE DATA
Crystal growpH: 8.5
Details: 0.1M TRIS PH 8.5, 0.1M LI2SO4, 0.1M NACL, 0.009% DDM, 3% 1,6-HEXANEDIOL AND 10% (W/V) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.7→49.63 Å / Num. obs: 122882 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 3.7 % / Biso Wilson estimate: 68.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WDQ

2wdq


Resolution: 2.7→48.85 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 19.943 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DENSITY FOR THE N-TERMINUS OF SDH C (RESIDUES 1-7 OF CHAINS C, G, K) AND THE N-TERMINUS OF SDHD (RESIDUES 1-10 OF CHAINS D, H AND L) WAS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DENSITY FOR THE N-TERMINUS OF SDH C (RESIDUES 1-7 OF CHAINS C, G, K) AND THE N-TERMINUS OF SDHD (RESIDUES 1-10 OF CHAINS D, H AND L) WAS WEAK AND THESE REGIONS ARE NOT INCLUDED IN THE MODEL. THE SIDE CHAIN OF SDHD TRP113 IS TRUNCATED AT THE CBETA ATOM SINCE DENSITY FOR THE SIDE CHAIN WAS POOR. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22247 6188 5 %SELECTED TO BE IDENTICAL TO 2WDQ
Rwork0.19032 ---
obs0.19192 116577 99.58 %-
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: 57.822 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24507 0 423 128 25058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02225533
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.98834629
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.36453147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17723.3881107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.133154203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.30615192
X-RAY DIFFRACTIONr_chiral_restr0.0940.23837
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02119230
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3351.515645
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.68225140
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.42339888
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1434.59438
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
11A4522tight positional0.060.05
12E4522tight positional0.050.05
13I4522tight positional0.050.05
21B1865tight positional0.050.05
22F1865tight positional0.050.05
23J1865tight positional0.050.05
31C947tight positional0.040.05
32G947tight positional0.040.05
33K947tight positional0.040.05
41D835tight positional0.040.05
42H835tight positional0.030.05
43L835tight positional0.040.05
11A4522tight thermal0.110.5
12E4522tight thermal0.090.5
13I4522tight thermal0.090.5
21B1865tight thermal0.120.5
22F1865tight thermal0.10.5
23J1865tight thermal0.10.5
31C947tight thermal0.090.5
32G947tight thermal0.070.5
33K947tight thermal0.070.5
41D835tight thermal0.080.5
42H835tight thermal0.070.5
43L835tight thermal0.070.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 419 -
Rwork0.286 8281 -
obs--96.59 %
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)
11.0346-0.1310.07441.4604-0.21251.5701-0.0076-0.09650.00570.1917-0.03060.2465-0.058-0.21440.0383-0.40460.02480.0608-0.16-0.0207-0.12931.653-11.16-24.224
21.6747-0.1799-0.19731.9822-0.54261.3931-0.03170.06850.15880.1806-0.0213-0.207-0.11820.19030.053-0.4198-0.0028-0.045-0.1547-0.007-0.158329.037-8.587-30.591
35.1562-0.43260.92391.04810.03431.31170.0354-0.06880.55470.1164-0.04-0.6531-0.13630.39180.0046-0.281-0.0662-0.03650.07890.00860.335661.191-4.932-31.635
43.9829-0.7491.37731.4469-0.34713.6007-0.08210.42850.0255-0.04610.0766-0.5734-0.18440.83260.0056-0.377-0.01980.01130.1753-0.00130.294467.184-17.635-37.974
51.46150.3940.38321.71270.54721.51140.1946-0.0835-0.15770.455-0.10830.13680.3221-0.1095-0.0863-0.0811-0.0572-0.0523-0.15920.01-0.109312.591-72.44-26.774
61.91090.5420.15891.3930.09151.66270.14490.0189-0.0910.32920.0185-0.31490.31460.1975-0.1634-0.16150.0559-0.1894-0.1078-0.0512-0.076738.569-61.29-26.356
74.04770.7233-0.99361.8495-0.46381.60680.2225-0.0103-0.47090.1944-0.1859-0.99210.31130.5732-0.0366-0.1570.1693-0.29230.2105-0.05770.540970.175-53.995-28.66
82.14420.5042-0.84432.21780.84464.29330.06470.16670.01680.09280.1997-0.95130.04150.8766-0.2645-0.30230.0948-0.13360.2971-0.05310.436371.491-41.239-37.154
91.9817-0.1110.37432.04360.19111.4970.03990.3654-0.023-0.58640.02780.26490.0536-0.2114-0.0677-0.01870.0453-0.14120.1929-0.0539-0.15946.033-39.982-79.962
102.20290.01150.15871.91690.38011.35670.06370.3167-0.0297-0.51450.0574-0.28890.05340.2848-0.121-0.09080.09310.10070.1275-0.033-0.198633.795-39.145-74.723
112.76011.21450.84322.05880.38481.4247-0.04030.6508-0.0498-0.42180.1672-0.5163-0.10920.7381-0.1269-0.04490.08560.33170.7567-0.02990.200165.499-32.381-72.949
122.78760.27970.25363.7472-0.11772.41630.1120.2602-0.0534-0.2481-0.0082-0.9457-0.2160.7311-0.1038-0.25480.0020.19410.6216-0.12270.246769.101-30.134-58.162
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 588
2X-RAY DIFFRACTION2B1 - 238
3X-RAY DIFFRACTION3C8 - 129
4X-RAY DIFFRACTION4D11 - 115
5X-RAY DIFFRACTION5E1 - 588
6X-RAY DIFFRACTION6F1 - 238
7X-RAY DIFFRACTION7G8 - 129
8X-RAY DIFFRACTION8H11 - 115
9X-RAY DIFFRACTION9I1 - 588
10X-RAY DIFFRACTION10J1 - 238
11X-RAY DIFFRACTION11K8 - 129
12X-RAY DIFFRACTION12L11 - 115

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