[English] 日本語
Yorodumi
- PDB-6n7l: Crystal structure of an alcohol dehydrogenase from Elizabethkingi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6n7l
TitleCrystal structure of an alcohol dehydrogenase from Elizabethkingia anophelis NUHP1
ComponentsAlcohol dehydrogenase
KeywordsOXIDOREDUCTASE / NIAID / National Institute of Allergy and Infectious Disease / zinc-dependent enzyme / metalloenzyme / unknown substrate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


alcohol dehydrogenase / oxidoreductase activity / nucleotide binding / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / alcohol dehydrogenase
Similarity search - Component
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of an alcohol dehydrogenase from Elizabethkingia anophelis NUHP1
Authors: Edwards, T.E. / Dranow, D.M. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionNov 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.2Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_symm_contact ...pdbx_entry_details / pdbx_validate_symm_contact / struct_conn / struct_conn_type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alcohol dehydrogenase
B: Alcohol dehydrogenase
C: Alcohol dehydrogenase
D: Alcohol dehydrogenase
E: Alcohol dehydrogenase
F: Alcohol dehydrogenase
G: Alcohol dehydrogenase
H: Alcohol dehydrogenase
I: Alcohol dehydrogenase
J: Alcohol dehydrogenase
K: Alcohol dehydrogenase
L: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,513150
Polymers452,97112
Non-polymers15,542138
Water40,3182238
1
A: Alcohol dehydrogenase
B: Alcohol dehydrogenase
C: Alcohol dehydrogenase
D: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,66858
Polymers150,9904
Non-polymers5,67754
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-62 kcal/mol
Surface area47010 Å2
MethodPISA
2
E: Alcohol dehydrogenase
F: Alcohol dehydrogenase
G: Alcohol dehydrogenase
H: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,29552
Polymers150,9904
Non-polymers5,30548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10550 Å2
ΔGint-61 kcal/mol
Surface area46200 Å2
MethodPISA
3
I: Alcohol dehydrogenase
J: Alcohol dehydrogenase
K: Alcohol dehydrogenase
L: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,55040
Polymers150,9904
Non-polymers4,56036
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10570 Å2
ΔGint-61 kcal/mol
Surface area45640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.150, 168.290, 199.730
Angle α, β, γ (deg.)90.000, 97.970, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 2 and (name N or name...
21(chain B and ((resid 2 and (name N or name...
31(chain C and ((resid 2 and (name N or name...
41(chain D and ((resid 2 and (name N or name...
51(chain E and (resid 2 through 10 or (resid 11...
61(chain F and ((resid 2 and (name N or name...
71(chain G and (resid 2 through 10 or (resid 11...
81(chain H and ((resid 2 and (name N or name...
91(chain I and (resid 2 through 10 or (resid 11...
101(chain J and ((resid 2 and (name N or name...
111(chain K and ((resid 2 and (name N or name...
121(chain L and (resid 2 through 17 or (resid 18...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 2 and (name N or name...A2
121(chain A and ((resid 2 and (name N or name...A1 - 501
131(chain A and ((resid 2 and (name N or name...A1 - 501
141(chain A and ((resid 2 and (name N or name...A1 - 501
151(chain A and ((resid 2 and (name N or name...A1 - 501
211(chain B and ((resid 2 and (name N or name...B2
221(chain B and ((resid 2 and (name N or name...B1 - 501
231(chain B and ((resid 2 and (name N or name...B1 - 501
241(chain B and ((resid 2 and (name N or name...B1 - 501
251(chain B and ((resid 2 and (name N or name...B1 - 501
311(chain C and ((resid 2 and (name N or name...C2
321(chain C and ((resid 2 and (name N or name...C-1 - 501
331(chain C and ((resid 2 and (name N or name...C-1 - 501
341(chain C and ((resid 2 and (name N or name...C-1 - 501
351(chain C and ((resid 2 and (name N or name...C-1 - 501
411(chain D and ((resid 2 and (name N or name...D2
421(chain D and ((resid 2 and (name N or name...D1 - 501
431(chain D and ((resid 2 and (name N or name...D1 - 501
441(chain D and ((resid 2 and (name N or name...D1 - 501
451(chain D and ((resid 2 and (name N or name...D1 - 501
511(chain E and (resid 2 through 10 or (resid 11...E2 - 10
521(chain E and (resid 2 through 10 or (resid 11...E11 - 12
531(chain E and (resid 2 through 10 or (resid 11...E2 - 501
541(chain E and (resid 2 through 10 or (resid 11...E2 - 501
551(chain E and (resid 2 through 10 or (resid 11...E2 - 501
561(chain E and (resid 2 through 10 or (resid 11...E2 - 501
611(chain F and ((resid 2 and (name N or name...F2
621(chain F and ((resid 2 and (name N or name...F0 - 501
631(chain F and ((resid 2 and (name N or name...F0 - 501
641(chain F and ((resid 2 and (name N or name...F0 - 501
651(chain F and ((resid 2 and (name N or name...F0 - 501
711(chain G and (resid 2 through 10 or (resid 11...G2 - 10
721(chain G and (resid 2 through 10 or (resid 11...G11 - 12
731(chain G and (resid 2 through 10 or (resid 11...G2 - 501
741(chain G and (resid 2 through 10 or (resid 11...G2 - 501
751(chain G and (resid 2 through 10 or (resid 11...G2 - 501
761(chain G and (resid 2 through 10 or (resid 11...G2 - 501
811(chain H and ((resid 2 and (name N or name...H2
821(chain H and ((resid 2 and (name N or name...H1 - 501
831(chain H and ((resid 2 and (name N or name...H1 - 501
841(chain H and ((resid 2 and (name N or name...H1 - 501
851(chain H and ((resid 2 and (name N or name...H1 - 501
911(chain I and (resid 2 through 10 or (resid 11...I2 - 10
921(chain I and (resid 2 through 10 or (resid 11...I11 - 12
931(chain I and (resid 2 through 10 or (resid 11...I1 - 501
941(chain I and (resid 2 through 10 or (resid 11...I1 - 501
951(chain I and (resid 2 through 10 or (resid 11...I1 - 501
961(chain I and (resid 2 through 10 or (resid 11...I1 - 501
1011(chain J and ((resid 2 and (name N or name...J2
1021(chain J and ((resid 2 and (name N or name...J1 - 501
1031(chain J and ((resid 2 and (name N or name...J1 - 501
1041(chain J and ((resid 2 and (name N or name...J1 - 501
1051(chain J and ((resid 2 and (name N or name...J1 - 501
1111(chain K and ((resid 2 and (name N or name...K2
1121(chain K and ((resid 2 and (name N or name...K1 - 501
1131(chain K and ((resid 2 and (name N or name...K1 - 501
1141(chain K and ((resid 2 and (name N or name...K1 - 501
1151(chain K and ((resid 2 and (name N or name...K1 - 501
1211(chain L and (resid 2 through 17 or (resid 18...L2 - 17
1221(chain L and (resid 2 through 17 or (resid 18...L18 - 19
1231(chain L and (resid 2 through 17 or (resid 18...L2 - 501
1241(chain L and (resid 2 through 17 or (resid 18...L2 - 501
1251(chain L and (resid 2 through 17 or (resid 18...L2 - 501
1261(chain L and (resid 2 through 17 or (resid 18...L2 - 501

-
Components

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Alcohol dehydrogenase


Mass: 37747.566 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Gene: BD94_3066 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A077EGR8

-
Non-polymers , 5 types, 2376 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 90 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2238 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: ElanA.10611.a.B1.PS38362 at 27.1 mg/mL with 2 mM NAD against 20% PEG 3350 and 0.2 M NaSCN then supplemented with 20% ethylene glycol for cryo-protection; crystal ID 299504a10; unique puck ID ntb9-5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→48.794 Å / Num. obs: 266429 / % possible obs: 99.9 % / Redundancy: 4.282 % / Biso Wilson estimate: 38.576 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.106 / Χ2: 0.981 / Net I/σ(I): 9.8 / Num. measured all: 1140923 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.154.2780.552.548414919681196690.8210.62899.9
2.15-2.214.2820.4583.058223119220192040.8630.52499.9
2.21-2.284.2860.3863.587991718647186460.8990.441100
2.28-2.354.2910.3114.367770518119181090.9340.35599.9
2.35-2.424.2920.2724.977532717552175510.9440.311100
2.42-2.514.2990.2365.757307317005169980.9550.269100
2.51-2.64.2980.26.667053916415164110.9680.228100
2.6-2.714.2970.1627.996764615748157410.9770.185100
2.71-2.834.2980.1389.296493115120151090.9820.15799.9
2.83-2.974.2960.11710.786207014458144490.9860.13399.9
2.97-3.134.2940.10212.265909613765137640.9890.116100
3.13-3.324.2830.08514.255597713073130710.9910.097100
3.32-3.554.2730.07516.125218812224122140.9930.08599.9
3.55-3.834.2810.06617.834876111389113910.9940.075100
3.83-4.24.2730.06219.214492810519105140.9930.071100
4.2-4.74.2820.05820.240880955095480.9940.066100
4.7-5.424.270.06119.9835853839983960.9940.069100
5.42-6.644.2550.0619.9230161708970880.9940.068100
6.64-9.394.2120.05720.9623249552455200.9940.06599.9
9.39-48.7944.0320.05821.3512242308530360.9930.06798.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3s2e

3s2e


Resolution: 2.1→48.794 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1909 15381 6.06 %
Rwork0.149 238494 -
obs0.1515 253875 95.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.95 Å2 / Biso mean: 40.4294 Å2 / Biso min: 13.19 Å2
Refinement stepCycle: final / Resolution: 2.1→48.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29996 0 928 2242 33166
Biso mean--40.98 41.44 -
Num. residues----4102
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10896X-RAY DIFFRACTION1.83TORSIONAL
12B10896X-RAY DIFFRACTION1.83TORSIONAL
13C10896X-RAY DIFFRACTION1.83TORSIONAL
14D10896X-RAY DIFFRACTION1.83TORSIONAL
15E10896X-RAY DIFFRACTION1.83TORSIONAL
16F10896X-RAY DIFFRACTION1.83TORSIONAL
17G10896X-RAY DIFFRACTION1.83TORSIONAL
18H10896X-RAY DIFFRACTION1.83TORSIONAL
19I10896X-RAY DIFFRACTION1.83TORSIONAL
110J10896X-RAY DIFFRACTION1.83TORSIONAL
111K10896X-RAY DIFFRACTION1.83TORSIONAL
112L10896X-RAY DIFFRACTION1.83TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0999-2.12370.27395200.2167255777587
2.1237-2.14870.26234460.20357222766887
2.1487-2.17490.24064920.20017421791389
2.1749-2.20250.24515190.18967311783089
2.2025-2.23140.22334830.18927474795790
2.2314-2.2620.26774840.19057513799790
2.262-2.29430.23875240.18027507803191
2.2943-2.32860.22275090.17297705821492
2.3286-2.3650.22344760.17037707818393
2.365-2.40370.22215050.1697864836994
2.4037-2.44520.22934740.17017726820093
2.4452-2.48960.22875340.1597825835994
2.4896-2.53750.21684980.15947902840095
2.5375-2.58930.21635090.16478042855196
2.5893-2.64560.21645010.16057977847896
2.6456-2.70710.22285130.15898039855296
2.7071-2.77480.2195700.15798082865297
2.7748-2.84990.20284650.15278143860897
2.8499-2.93370.20795660.15758142870898
2.9337-3.02840.21625210.16368192871398
3.0284-3.13660.22025010.1728205870699
3.1366-3.26220.2244800.16448349882999
3.2622-3.41060.20045530.16148264881799
3.4106-3.59040.19445740.154182848858100
3.5904-3.81520.17585340.142183338867100
3.8152-4.10970.14845170.121583868903100
4.1097-4.5230.13755240.106483538877100
4.523-5.17680.14195290.114983938922100
5.1768-6.51980.16425280.128384118939100
6.5198-48.80730.15015320.13698467899999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.26541.3601-0.24223.0066-0.73631.5942-0.16470.239-0.209-0.14290.0495-0.00880.175-0.01270.12070.3394-0.0989-0.00160.2603-0.01260.22475.9083-0.1647100.0057
21.80690.8896-0.29272.3203-0.30671.0715-0.0829-0.0451-0.4134-0.04480.0110.10460.3381-0.19140.05420.4212-0.14590.01170.29490.02430.3734-5.524-18.0006110.6597
32.9111-0.1505-2.73091.41580.05513.7177-0.08080.42450.4239-0.4550.0398-0.0949-0.3599-0.1505-0.01610.8485-0.2255-0.16980.46740.15960.410720.313934.419690.2828
41.91350.1435-0.48111.019-0.30741.1716-0.12040.14570.253-0.10260.06860.0151-0.34650.10040.03750.5039-0.1521-0.08340.2480.03220.310916.026825.5849100.8287
51.534-0.34740.13052.3894-0.24720.8605-0.1187-0.03190.2535-0.06540.104-0.1911-0.2940.24640.03270.4092-0.1724-0.04250.3177-0.01110.2324.91418.2896108.0922
61.577-0.4640.09462.08730.39112.6586-0.1142-0.0312-0.08560.00010.0578-0.24860.14920.5442-0.0120.2933-0.04240.00750.2890.02720.231928.503-1.5135105.7729
71.8872.3055-1.38116.4688-2.96312.9135-0.06680.2037-0.2659-0.4063-0.0643-0.06040.31310.12470.11660.3368-0.04530.010.2628-0.02820.269814.6789-3.695899.75
80.9368-0.67970.2411.3099-0.96111.506-0.1744-0.14740.05840.08310.0855-0.1685-0.30640.18450.08410.3504-0.11960.00050.26070.0020.208418.595413.0747112.2116
91.27220.6788-0.60433.5519-2.4311.6803-0.33710.28710.1073-0.43950.016-0.5023-0.34940.80270.33720.5166-0.26130.010.49660.05960.385733.806120.425796.223
104.2598-0.6389-5.41523.349-1.10168.70690.5232-0.6711.33090.75590.06540.0797-1.67830.4233-0.54470.93540.1268-0.11310.5754-0.27051.0088-13.039541.8273128.5253
113.9183-0.548-0.9342.0508-0.03241.9560.0017-0.23030.81720.14650.03130.2751-0.5522-0.3627-0.00350.48220.0602-0.03520.3844-0.10920.4474-7.484528.4796124.214
121.6724-0.09390.31981.6367-0.63031.3373-0.03-0.64810.14790.42120.00150.2665-0.1011-0.51790.03790.4337-0.06540.09370.5847-0.08840.273-8.853310.3785135.2729
132.5916-0.0996-1.69475.2937-0.10212.73560.1788-0.32320.43270.9767-0.06140.2552-0.7349-0.0925-0.16060.53910.0625-0.01820.3291-0.17970.4016-10.748432.640684.0698
141.5872-0.1155-0.62831.7840.06281.36640.1112-0.10390.26420.1943-0.0690.0634-0.3355-0.0892-0.03760.32660.02120.00620.1684-0.05210.2812-6.662323.803573.8511
151.6966-1.1779-0.7054.44460.83852.17190.02950.09290.05580.1784-0.1110.3764-0.1759-0.34340.06370.19050.02440.00190.1833-0.02710.204-13.233912.668.1676
161.60520.21950.37281.7047-0.262.34170.0637-0.1422-0.07960.2118-0.01860.17540.1138-0.2655-0.03830.2124-0.02290.02280.19680.00470.2026-15.6787-3.832572.113
175.821-6.4109-3.80427.27973.94642.7422-0.3665-0.367-0.39430.74590.23230.46320.40850.22670.17580.2765-0.0309-0.0170.22750.00770.1768-1.6056-5.736779.8844
180.3445-0.1091-0.4292.56490.12710.48240.0310.01740.05860.1223-0.00010.0635-0.188-0.088-0.02960.24360.01830.00710.1879-0.00770.2041-6.97618.649565.1518
192.4695-0.28420.70043.20311.41044.14250.1099-0.40670.21270.5426-0.09840.4501-0.1364-0.41220.0190.30430.02030.15920.3562-0.07420.3728-22.736216.695980.4779
202.34910.5705-2.29342.50761.34885.02740.25680.2720.7123-0.18340.1705-0.0846-1.0087-0.0563-0.40740.5194-0.0802-0.02230.31190.16950.596522.674937.61644.4046
212.34880.4266-0.59841.51030.0521.64760.0850.05190.48280.075-0.0328-0.0953-0.33830.1467-0.05380.2643-0.0365-0.01150.18210.04060.354317.038326.462950.7241
222.7881.7216-0.07864.39780.49141.77130.0040.09380.2708-0.02950.024-0.0719-0.09240.3080.00890.1667-0.0073-0.00770.2060.04080.212821.301412.981851.3108
231.82960.12180.26791.28430.29192.04690.01990.1672-0.0515-0.0853-0.061-0.15490.14690.28760.04130.18090.05910.0230.22660.03310.230920.9381-0.731741.1168
246.7225.61890.48634.69090.44160.8862-0.20230.3332-0.0774-0.54520.0808-0.19950.08290.14750.07790.2340.0720.0110.22290.02210.2057.07012.9733.7206
250.85850.22820.08083.24410.86981.5447-0.0049-0.04770.03780.1868-0.1048-0.0282-0.02950.26220.10330.1455-0.01910.01120.17210.03280.184414.33229.340252.6839
262.39241.13-0.13813.793-0.84371.5277-0.04940.26990.3885-0.3189-0.0719-0.393-0.21260.56990.13450.2153-0.0450.06090.42740.11350.397431.721319.870241.3989
273.38092.520.49787.4106-2.38091.62280.1106-0.0222-0.04210.0975-0.09310.30210.0685-0.2381-0.05830.3096-0.0710.08380.3349-0.16170.262-15.4288-27.816525.6463
280.87830.07850.05853.0811-0.31171.7352-0.04010.1288-0.24180.0108-0.03-0.02650.1444-0.12430.04040.2087-0.03880.0030.2724-0.08650.3018-13.3792-24.928832.509
291.07190.2662-0.08121.39420.39930.8754-0.02230.1146-0.23670.0732-0.0141-0.05370.2291-0.11280.03650.2201-0.0153-0.00130.1947-0.0530.2326-9.2936-19.932240.886
301.12150.1942-0.00471.9682-0.29681.9090.01420.13440.0896-0.00130.04570.1464-0.1252-0.188-0.06380.1580.05270.00880.23160.01260.2136-15.01026.925540.3243
311.25030.8563-0.07962.2458-0.06220.54160.0110.2533-0.0046-0.02160.0258-0.0448-0.0284-0.0598-0.03210.1750.0367-0.01230.2047-0.01140.1796-3.31011.795540.9542
322.45320.07970.09622.78451.23833.09370.05010.3472-0.1828-0.2659-0.07420.31370.121-0.48450.04770.1801-0.0046-0.04390.331-0.05490.2482-22.5733-11.688530.7795
332.2991-1.02632.65843.2247-1.11393.07610.1633-0.3468-0.55280.47120.29470.13230.4087-0.5533-0.37120.51920.08710.03990.28060.13680.516612.9748-40.920271.7652
341.84-0.9340.20721.895-0.0440.99830.0255-0.1036-0.42240.0542-0.01570.02310.31710.1172-0.00420.32680.0566-0.02010.17320.03340.29911.6752-26.872464.8742
352.2487-0.6267-0.13922.6626-0.18773.67060.052-0.2294-0.11120.1512-0.0329-0.17320.01740.3075-0.01810.1501-0.0192-0.03070.21310.03080.201421.1019-3.336374.7451
361.6972-0.772-0.56131.9880.93821.34650.0164-0.1931-0.11230.1062-0.0426-0.01360.09360.14960.04280.2007-0.0027-0.02890.15320.04190.17718.6554-5.659572.5523
371.6409-0.33280.26063.7602-2.14643.9286-0.0601-0.3053-0.32530.3739-0.0284-0.43030.26860.30580.0940.33930.1164-0.0910.3270.08180.39925.0776-25.467875.6249
385.26482.8585-5.05291.9868-1.71057.64940.48690.03711.84760.02310.6269-0.0878-0.9275-0.1519-0.99460.6509-0.0094-0.0510.419-0.01831.425126.822963.48096.124
394.6289-0.4372-1.19561.98320.75550.52710.0469-0.12231.3660.09810.227-0.5311-0.25090.1903-0.05130.34790.0111-0.05470.31360.04050.703521.030253.60115.7431
405.7054-0.125-0.96772.15460.77881.9163-0.0605-0.28950.83080.24690.1641-0.3778-0.14020.2488-0.10380.31010.0398-0.06090.25820.03250.416916.483749.97937.7967
417.02631.38250.96863.24121.7392.52420.0092-0.05840.12670.14880.0251-0.3798-0.060.2343-0.0670.21680.055-0.00470.27360.10860.320920.125839.6581-0.0694
421.7144-0.21230.22511.39280.2311.50690.0290.23390.0998-0.1436-0.0459-0.19120.01120.1588-0.00390.210.09010.04250.34570.09990.287419.700532.1877-14.8066
430.94230.1139-0.1710.82760.63810.90020.03620.21310.1749-0.1333-0.0997-0.0775-0.1061-0.03240.05160.22080.07190.0230.31090.10710.25789.295638.5954-11.219
442.19280.8379-0.65613.20510.30851.7539-0.05960.44180.7665-0.27320.1588-0.6721-0.30190.3271-0.08490.2508-0.01780.05380.47360.17610.798432.183547.7105-5.5348
452.54213.7978-1.16767.8609-1.49331.94920.2658-0.70670.19020.8238-0.35620.1266-0.42530.12140.07350.59720.1947-0.00230.5243-0.07450.2999-8.472247.30840.0399
461.63750.1255-0.37061.01380.11421.27110.0229-0.25660.27940.24750.03160.0402-0.3394-0.0951-0.04080.34750.12260.0170.24870.0080.2764-7.156343.110925.1112
471.16190.03970.362.028-0.20681.4009-0.00960.01680.04070.06210.10350.2694-0.0186-0.3916-0.0910.16620.06570.02550.34360.07380.2625-22.791625.306612.1241
481.2020.0631-0.91281.77481.8772.7227-0.0744-0.0991-0.17210.11580.1154-0.0290.2034-0.0535-0.04690.24270.04310.01680.26010.04650.2501-10.969916.356914.2735
491.30120.86480.23390.81950.69291.2689-0.04970.0190.1346-0.0170.03970.1707-0.2343-0.16410.00370.20270.0920.02280.24410.04110.2006-9.063935.474611.6974
502.0326-1.08090.14771.89711.34682.1026-0.0567-0.40220.14530.49270.23350.2922-0.3561-0.8111-0.01770.36870.14780.11940.49690.02960.3426-23.235638.621229.5784
511.9302-2.11611.30742.4022-1.31043.87030.07130.0898-1.1728-0.19980.27840.90880.9386-0.7683-0.25380.6407-0.14040.08790.4595-0.13691.0447-1.7302-13.7648-7.858
523.5008-1.6095-0.17952.57910.05031.06120.02820.4407-0.9689-0.1396-0.07560.31350.4051-0.07010.05440.34030.03540.03970.2941-0.10170.44870.79931.643-7.4145
531.5481-0.144-0.58521.51250.35532.8165-0.0667-0.0419-0.14240.1370.0041-0.10720.220.22440.04720.20180.09480.01190.23220.05530.259614.897914.373612.1142
541.4224-0.3553-0.79620.61660.95512.395-0.0872-0.0431-0.13150.0568-0.02330.04660.1791-0.00840.11570.2040.05960.02450.180.0560.23972.430316.30649.9266
552.0275-0.4522-0.07244.37810.38411.1458-0.1628-0.1378-0.88010.2663-0.0037-0.06860.55350.03020.1150.47380.12840.09730.30790.05940.642813.293-5.50572.3189
562.54940.52990.19233.1923-3.4474.2986-0.06171.3876-0.3802-0.74970.2204-0.00120.2967-0.138-0.0290.413-0.0128-0.01571.0064-0.05260.3982-21.819222.9943-38.7948
572.629-0.05570.68711.40610.03771.5007-0.03270.5555-0.0694-0.18230.0570.13920.0705-0.1596-0.02570.2220.0290.00270.48030.02370.2293-16.994924.9116-24.225
581.84550.20220.64742.17540.44391.3111-0.04860.43150.4906-0.08590.00440.2564-0.272-0.13790.07950.26990.12910.0350.38390.15690.3902-15.660748.2143-10.3368
591.28520.34070.12650.8080.20580.64110.02720.40110.298-0.10030.02060.0843-0.1196-0.0986-0.04870.25260.09420.01740.38020.1250.2697-5.416941.035-12.9823
601.5561-0.65951.56991.6735-0.08455.0887-0.1280.60420.3982-0.3814-0.03420.2084-0.3234-0.45240.14020.30890.0967-0.05260.73130.17950.4131-26.497738.9529-27.229
612.7977-0.30682.84293.11370.10633.40660.0973-1.2973-0.6780.78250.1555-0.02510.3165-0.8484-0.2830.9442-0.0505-0.12661.20370.47360.748927.2672-19.0267154.0753
622.5150.54980.27931.0451-0.18641.71410.1834-0.8375-0.68240.3967-0.2016-0.3030.3640.07520.04610.5948-0.088-0.10060.6060.23750.443123.5095-11.3951141.2703
632.1294-0.39910.03572.06770.80521.52060.0249-0.47240.15780.17520.0502-0.2248-0.21250.3151-0.03060.4337-0.1562-0.06150.48840.00170.245526.272815.5059137.3861
641.6738-0.49760.13452.35520.26181.95230.0189-0.7460.14590.3873-0.1846-0.0365-0.02050.10160.13020.5086-0.143-0.01050.5156-0.04520.229514.45916.463138.7129
652.6119-1.3282.13080.8725-1.22691.8416-0.3098-1.03290.56411.0590.0295-0.3404-0.5703-0.04030.21270.6193-0.1345-0.02710.7475-0.07030.30298.73514.1045143.3561
660.97160.08010.06561.0788-0.66161.57970.0685-0.596-0.17320.476-0.2184-0.40830.12820.41310.12080.5476-0.1151-0.12880.63580.13020.365128.7223-0.4862141.2143
671.68081.6795-0.20754.6837-1.61951.6053-0.1010.1046-0.6129-0.21850.111-0.13630.5560.22570.29070.6218-0.02780.11580.30890.03070.78413.2872-37.9112.1838
681.41830.58540.27241.8972-0.01660.89180.0423-0.1472-0.58440.149-0.0347-0.1310.3116-0.01980.01490.5006-0.10910.01930.28850.10710.45243.1049-23.5705117.2145
691.83250.09710.63261.9036-0.57473.69150.0097-0.0602-0.16190.0418-0.00090.09140.0779-0.3717-0.01040.2837-0.10920.03920.2794-0.00480.2143-8.2587-2.3992104.4208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'J' and (resid 245 through 280 )J245 - 280
2X-RAY DIFFRACTION2chain 'J' and (resid 281 through 343 )J281 - 343
3X-RAY DIFFRACTION3chain 'K' and (resid 1 through 31 )K1 - 31
4X-RAY DIFFRACTION4chain 'K' and (resid 32 through 119 )K32 - 119
5X-RAY DIFFRACTION5chain 'K' and (resid 120 through 190 )K120 - 190
6X-RAY DIFFRACTION6chain 'K' and (resid 191 through 263 )K191 - 263
7X-RAY DIFFRACTION7chain 'K' and (resid 264 through 280 )K264 - 280
8X-RAY DIFFRACTION8chain 'K' and (resid 281 through 304 )K281 - 304
9X-RAY DIFFRACTION9chain 'K' and (resid 305 through 342 )K305 - 342
10X-RAY DIFFRACTION10chain 'L' and (resid 2 through 31 )L2 - 31
11X-RAY DIFFRACTION11chain 'L' and (resid 32 through 164 )L32 - 164
12X-RAY DIFFRACTION12chain 'L' and (resid 165 through 341 )L165 - 341
13X-RAY DIFFRACTION13chain 'A' and (resid 1 through 31 )A1 - 31
14X-RAY DIFFRACTION14chain 'A' and (resid 32 through 143 )A32 - 143
15X-RAY DIFFRACTION15chain 'A' and (resid 144 through 164 )A144 - 164
16X-RAY DIFFRACTION16chain 'A' and (resid 165 through 263 )A165 - 263
17X-RAY DIFFRACTION17chain 'A' and (resid 264 through 280 )A264 - 280
18X-RAY DIFFRACTION18chain 'A' and (resid 281 through 304 )A281 - 304
19X-RAY DIFFRACTION19chain 'A' and (resid 305 through 342 )A305 - 342
20X-RAY DIFFRACTION20chain 'B' and (resid 1 through 31 )B1 - 31
21X-RAY DIFFRACTION21chain 'B' and (resid 32 through 143 )B32 - 143
22X-RAY DIFFRACTION22chain 'B' and (resid 144 through 164 )B144 - 164
23X-RAY DIFFRACTION23chain 'B' and (resid 165 through 263 )B165 - 263
24X-RAY DIFFRACTION24chain 'B' and (resid 264 through 280 )B264 - 280
25X-RAY DIFFRACTION25chain 'B' and (resid 281 through 304 )B281 - 304
26X-RAY DIFFRACTION26chain 'B' and (resid 305 through 342 )B305 - 342
27X-RAY DIFFRACTION27chain 'C' and (resid -1 through 18 )C-1 - 18
28X-RAY DIFFRACTION28chain 'C' and (resid 19 through 51 )C19 - 51
29X-RAY DIFFRACTION29chain 'C' and (resid 52 through 164 )C52 - 164
30X-RAY DIFFRACTION30chain 'C' and (resid 165 through 244 )C165 - 244
31X-RAY DIFFRACTION31chain 'C' and (resid 245 through 304 )C245 - 304
32X-RAY DIFFRACTION32chain 'C' and (resid 305 through 342 )C305 - 342
33X-RAY DIFFRACTION33chain 'D' and (resid 1 through 31 )D1 - 31
34X-RAY DIFFRACTION34chain 'D' and (resid 32 through 164 )D32 - 164
35X-RAY DIFFRACTION35chain 'D' and (resid 165 through 244 )D165 - 244
36X-RAY DIFFRACTION36chain 'D' and (resid 245 through 304 )D245 - 304
37X-RAY DIFFRACTION37chain 'D' and (resid 305 through 343 )D305 - 343
38X-RAY DIFFRACTION38chain 'E' and (resid 2 through 31 )E2 - 31
39X-RAY DIFFRACTION39chain 'E' and (resid 32 through 99 )E32 - 99
40X-RAY DIFFRACTION40chain 'E' and (resid 100 through 143 )E100 - 143
41X-RAY DIFFRACTION41chain 'E' and (resid 144 through 164 )E144 - 164
42X-RAY DIFFRACTION42chain 'E' and (resid 165 through 244 )E165 - 244
43X-RAY DIFFRACTION43chain 'E' and (resid 245 through 304 )E245 - 304
44X-RAY DIFFRACTION44chain 'E' and (resid 305 through 341 )E305 - 341
45X-RAY DIFFRACTION45chain 'F' and (resid 0 through 31 )F0 - 31
46X-RAY DIFFRACTION46chain 'F' and (resid 32 through 164 )F32 - 164
47X-RAY DIFFRACTION47chain 'F' and (resid 165 through 244 )F165 - 244
48X-RAY DIFFRACTION48chain 'F' and (resid 245 through 280 )F245 - 280
49X-RAY DIFFRACTION49chain 'F' and (resid 281 through 304 )F281 - 304
50X-RAY DIFFRACTION50chain 'F' and (resid 305 through 342 )F305 - 342
51X-RAY DIFFRACTION51chain 'G' and (resid 2 through 31 )G2 - 31
52X-RAY DIFFRACTION52chain 'G' and (resid 32 through 164 )G32 - 164
53X-RAY DIFFRACTION53chain 'G' and (resid 165 through 244 )G165 - 244
54X-RAY DIFFRACTION54chain 'G' and (resid 245 through 304 )G245 - 304
55X-RAY DIFFRACTION55chain 'G' and (resid 305 through 341 )G305 - 341
56X-RAY DIFFRACTION56chain 'H' and (resid 1 through 31 )H1 - 31
57X-RAY DIFFRACTION57chain 'H' and (resid 32 through 164 )H32 - 164
58X-RAY DIFFRACTION58chain 'H' and (resid 165 through 244 )H165 - 244
59X-RAY DIFFRACTION59chain 'H' and (resid 245 through 304 )H245 - 304
60X-RAY DIFFRACTION60chain 'H' and (resid 305 through 342 )H305 - 342
61X-RAY DIFFRACTION61chain 'I' and (resid 1 through 31 )I1 - 31
62X-RAY DIFFRACTION62chain 'I' and (resid 32 through 164 )I32 - 164
63X-RAY DIFFRACTION63chain 'I' and (resid 165 through 244 )I165 - 244
64X-RAY DIFFRACTION64chain 'I' and (resid 245 through 263 )I245 - 263
65X-RAY DIFFRACTION65chain 'I' and (resid 264 through 280 )I264 - 280
66X-RAY DIFFRACTION66chain 'I' and (resid 281 through 341 )I281 - 341
67X-RAY DIFFRACTION67chain 'J' and (resid 1 through 31 )J1 - 31
68X-RAY DIFFRACTION68chain 'J' and (resid 32 through 164 )J32 - 164
69X-RAY DIFFRACTION69chain 'J' and (resid 165 through 244 )J165 - 244

+
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