[English] 日本語
Yorodumi
- PDB-2ws3: Crystal structure of the E. coli succinate:quinone oxidoreductase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ws3
TitleCrystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhD Tyr83Phe mutant
Components(SUCCINATE DEHYDROGENASE ...) x 4
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT
Function / homology
Function and homology information


plasma membrane succinate dehydrogenase complex / succinate dehydrogenase complex / succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / : / succinate dehydrogenase / cytochrome complex assembly / aerobic electron transport chain / oxidoreductase activity, acting on the CH-CH group of donors / anaerobic respiration ...plasma membrane succinate dehydrogenase complex / succinate dehydrogenase complex / succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / : / succinate dehydrogenase / cytochrome complex assembly / aerobic electron transport chain / oxidoreductase activity, acting on the CH-CH group of donors / anaerobic respiration / ubiquinone binding / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / aerobic respiration / tricarboxylic acid cycle / 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 b556 subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / 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 b556 subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / 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 / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Fumarate reductase / succinate dehydrogenase FAD-binding site. / 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 / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Ubiquitin-like (UB roll) / 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: 3.2 Å
AuthorsRuprecht, J. / Yankovskaya, V. / Maklashina, E. / Iwata, S. / Cecchini, G.
CitationJournal: To be Published
Title: Succinate Dehydrogenase Activity
Authors: Ruprecht, J. / Yankovskaya, V. / Maklashina, E. / Iwata, S. / Cecchini, G.
History
DepositionSep 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 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.pdbx_dist_value / _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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
B: SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
C: SUCCINATE DEHYDROGENASE CYTOCHROME B-556 SUBUNIT
D: SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT
E: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
F: SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
G: SUCCINATE DEHYDROGENASE CYTOCHROME B-556 SUBUNIT
H: SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT
I: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
J: SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
K: SUCCINATE DEHYDROGENASE CYTOCHROME B-556 SUBUNIT
L: SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,27336
Polymers355,42612
Non-polymers7,84724
Water0
1
I: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
J: SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
K: SUCCINATE DEHYDROGENASE CYTOCHROME B-556 SUBUNIT
L: SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,09112
Polymers118,4754
Non-polymers2,6168
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15680 Å2
ΔGint-163.4 kcal/mol
Surface area37780 Å2
MethodPISA
2
E: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
F: SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
G: SUCCINATE DEHYDROGENASE CYTOCHROME B-556 SUBUNIT
H: SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,09112
Polymers118,4754
Non-polymers2,6168
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15610 Å2
ΔGint-158.7 kcal/mol
Surface area37770 Å2
MethodPISA
3
A: SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
B: SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
C: SUCCINATE DEHYDROGENASE CYTOCHROME B-556 SUBUNIT
D: SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,09112
Polymers118,4754
Non-polymers2,6168
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15620 Å2
ΔGint-160.2 kcal/mol
Surface area37720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.850, 184.710, 203.310
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
13GLNGLNVALVALCC8 - 1288 - 128
23GLNGLNVALVALGG8 - 1288 - 128
33GLNGLNVALVALKK8 - 1288 - 128
14ASNASNVALVALDD11 - 11511 - 115
24ASNASNVALVALHH11 - 11511 - 115
34ASNASNVALVALLL11 - 11511 - 115

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.94492, 0.28619, 0.15879), (0.28093, -0.46029, -0.84215), (-0.16793, 0.84038, -0.51533)18.50396, -97.15851, -30.96337
2given(0.94703, 0.2816, -0.15436), (0.27136, -0.44471, 0.85358), (0.17172, -0.85026, -0.49757)4.53321, -22.49522, -101.68967
3given(0.94805, 0.28095, 0.14925), (0.26963, -0.46063, -0.84565), (-0.16883, 0.84196, -0.51245)18.16462, -97.08932, -30.9092
4given(0.94465, 0.2817, -0.16817), (0.28418, -0.44644, 0.84849), (0.16394, -0.84932, -0.50178)4.2652, -23.09317, -101.58215
5given(0.94733, 0.28472, 0.14666), (0.26841, -0.45598, -0.84855), (-0.17472, 0.84322, -0.50838)18.2494, -97.04973, -30.63527
6given(0.94231, 0.28318, -0.17851), (0.29486, -0.44971, 0.8431), (0.15847, -0.8471, -0.50726)4.07432, -23.69032, -101.56531
7given(0.94619, 0.28688, 0.14975), (0.27114, -0.45021, -0.85076), (-0.17665, 0.84558, -0.50377)18.46492, -97.2653, -30.37287
8given(0.9441, 0.27693, -0.17882), (0.29068, -0.44353, 0.84781), (0.15548, -0.8524, -0.49924)3.82943, -23.20065, -101.13769

-
Components

-
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
#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
#3: Protein 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 8-128 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


Mass: 12858.438 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

-
Non-polymers , 8 types, 24 molecules

#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-TEO / MALATE LIKE INTERMEDIATE


Mass: 132.072 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H4O5
#8: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


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


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


Mass: 295.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe3S4
#11: 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 / Carboxin


Mass: 235.302 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H13NO2S
#12: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN D, TYR 83 TO PHE ENGINEERED RESIDUE IN CHAIN H, TYR 83 TO PHE ...ENGINEERED RESIDUE IN CHAIN D, TYR 83 TO PHE ENGINEERED RESIDUE IN CHAIN H, TYR 83 TO PHE ENGINEERED RESIDUE IN CHAIN L, TYR 83 TO PHE

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.67 % / Description: NONE
Crystal growpH: 8.5 / Details: PH 8.5

-
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: 3.2→49.03 Å / Num. obs: 71105 / % possible obs: 99.8 % / Observed criterion σ(I): 6 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.1
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.4 / % possible all: 100

-
Processing

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

2wdq


Resolution: 3.2→49.03 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.885 / SU B: 52.792 / SU ML: 0.412 / Cross valid method: THROUGHOUT / ESU R Free: 0.487 / 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
Rfree0.25271 3797 5.1 %IDENTICAL TO 2WDQ
Rwork0.2187 ---
obs0.22039 71105 99.77 %-
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: 72 Å2
Baniso -1Baniso -2Baniso -3
1--4.7 Å20 Å20 Å2
2--1.19 Å20 Å2
3---3.51 Å2
Refinement stepCycle: LAST / Resolution: 3.2→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24477 0 423 0 24900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02225501
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.98934581
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4253144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90723.3881107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.248154200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.77415192
X-RAY DIFFRACTIONr_chiral_restr0.0880.23831
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_it0.1391.515636
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.23225125
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.63839865
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8694.59405
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 positional0.050.05
12E4522tight positional0.040.05
13I4522tight positional0.040.05
21B1869tight positional0.050.05
22F1869tight positional0.040.05
23J1869tight positional0.040.05
31C933tight positional0.040.05
32G933tight positional0.040.05
33K933tight positional0.040.05
41D835tight positional0.040.05
42H835tight positional0.040.05
43L835tight positional0.030.05
11A4522tight thermal0.080.5
12E4522tight thermal0.070.5
13I4522tight thermal0.070.5
21B1869tight thermal0.10.5
22F1869tight thermal0.070.5
23J1869tight thermal0.080.5
31C933tight thermal0.060.5
32G933tight thermal0.050.5
33K933tight thermal0.060.5
41D835tight thermal0.070.5
42H835tight thermal0.060.5
43L835tight thermal0.060.5
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 289 -
Rwork0.3 5162 -
obs--99.84 %
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)
11.7033-0.02170.1771.9944-0.13651.81130.02990.01450.25760.3454-0.08020.4508-0.0047-0.2080.05030.0674-0.00720.10230.0384-0.00070.1941.2867-10.8839-23.6106
22.8210.06130.19993.2648-0.72211.7589-0.09680.36540.43080.4190.0342-0.3362-0.04670.21110.06260.0598-0.0002-0.05980.07620.04930.10428.6688-8.1688-29.765
34.7929-0.78760.33621.5258-0.1821.4693-0.0236-0.0610.6350.15960.0964-0.5230.02960.2758-0.07270.1713-0.0183-0.04740.24990.0050.576160.4974-4.4443-30.5164
43.5287-0.4842-0.36772.1208-0.52942.43750.16130.50770.2095-0.0489-0.1285-0.71780.04070.5794-0.03280.07950.05960.00290.3070.04840.548966.8484-16.6032-37.2742
51.6660.43470.29192.0360.20691.54260.10030.0905-0.4520.4611-0.00590.14370.2657-0.0288-0.09430.3590.0006-0.08860.0428-0.07530.271712.8631-71.9087-28.1864
62.71090.62620.0061.90280.18341.94380.10590.2247-0.26250.38910.0096-0.43360.31590.3368-0.11550.29410.1028-0.23330.1253-0.10610.262638.6012-60.4421-27.3896
73.95111.7228-1.43242.1538-0.47681.63160.14750.1301-0.8298-0.0255-0.1279-0.97570.30910.3971-0.01960.35830.2383-0.33130.4062-0.14570.870169.8194-52.8861-29.4649
81.94020.4883-0.32362.65760.19383.39430.20580.561-0.2986-0.1223-0.033-0.97410.08080.5372-0.17290.15050.1474-0.13640.4533-0.13710.723971.3585-39.9454-37.4617
91.8886-0.19930.06312.03580.15870.88530.03061.0057-0.0773-0.70760.11080.39060.061-0.2038-0.14130.75820.0487-0.24331.5265-0.08780.49146.3316-37.447-80.4759
102.60040.3612-0.12632.3094-0.04231.747-0.01411.0614-0.2244-0.68240.2131-0.0410.1689-0.0389-0.1990.54910.0853-0.04021.1139-0.11480.242934.037-36.5463-75.0261
112.65121.2428-0.06252.4007-0.0691.9598-0.04171.256-0.0547-0.56770.1239-0.3743-0.12690.2329-0.08210.61890.11140.23261.3439-0.13870.429765.2565-29.5913-72.7546
122.5586-0.06920.54223.9518-0.20652.07010.00960.8958-0.0548-0.1220.0607-0.8173-0.03210.6175-0.07040.25890.12040.1570.9204-0.08490.439269.0119-28.0028-57.9783
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 588
2X-RAY DIFFRACTION1A601
3X-RAY DIFFRACTION2B1 - 238
4X-RAY DIFFRACTION2B302 - 304
5X-RAY DIFFRACTION3C8 - 128
6X-RAY DIFFRACTION4D11 - 115
7X-RAY DIFFRACTION5E1 - 588
8X-RAY DIFFRACTION5E601
9X-RAY DIFFRACTION6F1 - 238
10X-RAY DIFFRACTION6F302 - 304
11X-RAY DIFFRACTION7G8 - 128
12X-RAY DIFFRACTION8H11 - 115
13X-RAY DIFFRACTION9I1 - 588
14X-RAY DIFFRACTION9I601
15X-RAY DIFFRACTION10J1 - 238
16X-RAY DIFFRACTION10J302 - 304
17X-RAY DIFFRACTION11K8 - 128
18X-RAY DIFFRACTION12L11 - 115

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more