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- PDB-2wu2: Crystal structure of the E. coli succinate:quinone oxidoreductase... -

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Basic information

Entry
Database: PDB / ID: 2wu2
TitleCrystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhC His84Met mutant
Components(SUCCINATE DEHYDROGENASE ...) x 4
KeywordsOXIDOREDUCTASE / CELL INNER MEMBRANE / TRICARBOXYLIC ACID CYCLE / METAL-BINDING / TRANSMEMBRANE / TRANSPORT / 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: 2.5 Å
AuthorsRuprecht, J. / Yankovskaya, V. / Maklashina, E. / Iwata, S. / Cecchini, G.
CitationJournal: To be Published
Title: Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhc His84met Mutant
Authors: Ruprecht, J. / Yankovskaya, V. / Maklashina, E. / Iwata, S. / Cecchini, G.
History
DepositionSep 28, 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 1.3Dec 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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

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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 PROTEIN SUBUNIT
E: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
F: SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
G: SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT
H: SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN SUBUNIT
I: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
J: SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
K: SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT
L: SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,30036
Polymers355,45312
Non-polymers7,84724
Water18,3391018
1
A: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
B: SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
C: SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT
D: SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,10012
Polymers118,4844
Non-polymers2,6168
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15540 Å2
ΔGint-157.9 kcal/mol
Surface area37770 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 PROTEIN SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,10012
Polymers118,4844
Non-polymers2,6168
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15580 Å2
ΔGint-157.4 kcal/mol
Surface area37800 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 PROTEIN SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,10012
Polymers118,4844
Non-polymers2,6168
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15550 Å2
ΔGint-156.1 kcal/mol
Surface area37840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.033, 183.363, 202.720
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(0.94731, 0.25986, -0.18727), (0.29252, -0.4637, 0.83631), (0.13049, -0.84703, -0.51529)3.41661, -26.42373, -101.08395
2given(0.95022, 0.27314, 0.14994), (0.26598, -0.46038, -0.84694), (-0.1623, 0.84466, -0.51011)19.06854, -99.14578, -30.12042
3given(0.95019, 0.24971, -0.18651), (0.28661, -0.46493, 0.83767), (0.12246, -0.8494, -0.51334)2.65864, -26.24914, -100.98786
4given(0.94958, 0.28294, 0.13506), (0.25762, -0.45865, -0.85046), (-0.17868, 0.84237, -0.50841)18.32764, -99.1377, -29.64193
5given(0.95001, 0.2472, -0.19073), (0.2882, -0.45926, 0.84025), (0.12012, -0.85321, -0.50754)2.30747, -25.93887, -100.95502
6given(0.94732, 0.29513, 0.12444), (0.25455, -0.4579, -0.85178), (-0.19441, 0.83858, -0.50891)18.01566, -99.04029, -29.22209
7given(0.95043, 0.24488, -0.19161), (0.28733, -0.45617, 0.84223), (0.11884, -0.85554, -0.50392)2.14672, -25.66306, -100.90508
8given(0.94849, 0.2908, 0.12569), (0.25222, -0.45311, -0.85503), (-0.19169, 0.84269, -0.50311)17.88715, -98.93965, -28.91714

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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: 26800.912 Da / Num. of mol.: 3
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 / CYTOCHROME B-556


Mass: 14306.148 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 PROTEIN SUBUNIT


Mass: 12874.438 Da / Num. of mol.: 3 / Mutation: YES
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, 1042 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.: 1018 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN C, HIS 84 TO MET ENGINEERED RESIDUE IN CHAIN G, HIS 84 TO MET ...ENGINEERED RESIDUE IN CHAIN C, HIS 84 TO MET ENGINEERED RESIDUE IN CHAIN G, HIS 84 TO MET ENGINEERED RESIDUE IN CHAIN K, HIS 84 TO MET
Has protein modificationY

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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: 60.33 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1M TRIS PH 8.5, 0.1M MGSO4, 11% PEG4000, 1MM CARBOXIN

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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: 2.5→48.74 Å / Num. obs: 153926 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WDQ

2wdq


Resolution: 2.5→48 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 13.601 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.23 / 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
Rfree0.21431 7724 5 %SELECTED TO BE IDENTICAL TO 2WDQ
Rwork0.17689 ---
obs0.17876 146098 99.7 %-
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: 26.086 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å20 Å2
2--1.27 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24519 0 423 1018 25960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02225551
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.98934647
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75853147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39223.3881107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.146154209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.09915192
X-RAY DIFFRACTIONr_chiral_restr0.1370.23834
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119269
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_it0.4441.515654
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.897225155
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.95339897
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8894.59441
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 positional0.070.05
12E4522tight positional0.050.05
13I4522tight positional0.050.05
21B1869tight positional0.050.05
22F1869tight positional0.050.05
23J1869tight positional0.050.05
31C946tight positional0.040.05
32G946tight positional0.040.05
33K946tight positional0.040.05
41D836tight positional0.040.05
42H836tight positional0.040.05
43L836tight positional0.040.05
11A4522tight thermal0.150.5
12E4522tight thermal0.130.5
13I4522tight thermal0.130.5
21B1869tight thermal0.170.5
22F1869tight thermal0.150.5
23J1869tight thermal0.140.5
31C946tight thermal0.10.5
32G946tight thermal0.080.5
33K946tight thermal0.080.5
41D836tight thermal0.10.5
42H836tight thermal0.10.5
43L836tight thermal0.10.5
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 547 -
Rwork0.231 10366 -
obs--96.99 %
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)
10.9102-0.08260.08881.3136-0.11451.40940.0366-0.10410.00410.162-0.0710.2017-0.0376-0.16750.03440.0252-0.01130.03490.0512-0.0430.11481.856-11.494-24.514
21.10330.32430.2021.42310.48811.37110.159-0.0673-0.15660.4039-0.08210.09170.2862-0.1005-0.07680.2932-0.055-0.07140.03290.03370.141912.742-72.373-26.872
31.448-0.03370.34211.64380.15461.19180.07070.1712-0.0485-0.4130.01130.20740.0682-0.1362-0.0820.25870.0248-0.10130.1891-0.03430.07645.889-40.08-79.711
41.4168-0.013-0.07281.4475-0.30681.50730.0163-0.00890.10550.1574-0.0507-0.2483-0.09430.17670.03430.0211-0.0107-0.03440.0497-0.01990.124329.027-9.388-30.537
51.51440.46760.34371.2320.4061.05830.11340.0041-0.07710.27430.0025-0.2490.23480.196-0.11590.20630.05-0.14910.0876-0.01840.174138.507-61.135-26.858
61.7828-0.20360.08811.4706-0.05120.9440.07550.2075-0.0059-0.3386-0.0161-0.21690.08020.2344-0.05940.20320.05950.05210.2001-0.04660.059433.531-38.963-74.565
75.1288-1.2374-0.03791.05140.18250.9595-0.0334-0.37920.67930.0880.0871-0.5516-0.10240.3323-0.05370.0849-0.0871-0.0540.2681-0.09160.548460.97-5.557-31.502
84.53631.3869-1.21841.9541-0.62721.54890.074-0.0826-0.58090.1807-0.1357-0.86930.26890.47220.06170.1910.1368-0.24070.327-0.01670.68570.002-54.107-29.358
94.25261.40951.53251.78220.76522.0704-0.13390.76860.1848-0.39250.1899-0.4635-0.14080.7976-0.0560.25660.03010.25060.73290.00590.413564.944-32.01-73.118
103.4915-0.29140.20581.0284-0.01771.4780.0110.1043-0.0307-0.04250.134-0.3912-0.1340.4749-0.1450.0215-0.0261-0.00120.3213-0.08550.447867-18.157-38.011
110.70620.7887-0.45322.62720.01472.86560.00420.102-0.06120.020.0683-0.84240.1650.5343-0.07240.03860.0857-0.07780.358-0.0460.59271.327-41.382-37.789
122.58320.27111.08273.02220.46431.3856-0.05790.24770.0868-0.26080.0638-0.7192-0.03050.5131-0.00590.07290.0050.12770.5547-0.0840.41668.682-29.971-58.343
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 588
2X-RAY DIFFRACTION2E1 - 588
3X-RAY DIFFRACTION3I1 - 588
4X-RAY DIFFRACTION4B1 - 238
5X-RAY DIFFRACTION5F1 - 238
6X-RAY DIFFRACTION6J1 - 238
7X-RAY DIFFRACTION7C8 - 129
8X-RAY DIFFRACTION8G8 - 129
9X-RAY DIFFRACTION9K8 - 129
10X-RAY DIFFRACTION10D11 - 115
11X-RAY DIFFRACTION11H11 - 115
12X-RAY DIFFRACTION12L11 - 115

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