[English] 日本語
Yorodumi
- PDB-2pnk: CRYSTAL STRUCTURE OF AN URONATE ISOMERASE (BH0493) FROM BACILLUS ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pnk
TitleCRYSTAL STRUCTURE OF AN URONATE ISOMERASE (BH0493) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION
ComponentsBH0493 protein
KeywordsISOMERASE / URONATE ISOMERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


uronate isomerase, domain 2, chain A / uronate isomerase, domain 2, chain A / Metal-dependent hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / PHOSPHATE ION / Unknown ligand / BH0493 protein
Similarity search - Component
Biological speciesBacillus halodurans C-125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MAD / MAD/molecular replacement / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein (NP_241359.1) from Bacillus halodurans at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 300 BIOMOLECULE: 1,2,3,4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 12 ... BIOMOLECULE: 1,2,3,4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 12 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TRIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE, FOLLOWED BY THE TARGET SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BH0493 protein
B: BH0493 protein
C: BH0493 protein
D: BH0493 protein
E: BH0493 protein
F: BH0493 protein
G: BH0493 protein
H: BH0493 protein
I: BH0493 protein
J: BH0493 protein
K: BH0493 protein
L: BH0493 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)614,80777
Polymers610,33312
Non-polymers4,47365
Water67,2323732
1
A: BH0493 protein
B: BH0493 protein
C: BH0493 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,45316
Polymers152,5833
Non-polymers87013
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13950 Å2
ΔGint-42 kcal/mol
Surface area42950 Å2
MethodPISA
2
D: BH0493 protein
E: BH0493 protein
F: BH0493 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,42015
Polymers152,5833
Non-polymers83712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13810 Å2
ΔGint-46 kcal/mol
Surface area41660 Å2
MethodPISA
3
G: BH0493 protein
H: BH0493 protein
I: BH0493 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,82622
Polymers152,5833
Non-polymers1,24319
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15630 Å2
ΔGint-66 kcal/mol
Surface area43200 Å2
MethodPISA
4
J: BH0493 protein
K: BH0493 protein
L: BH0493 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,10724
Polymers152,5833
Non-polymers1,52321
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15870 Å2
ΔGint-68 kcal/mol
Surface area43090 Å2
MethodPISA
5
A: BH0493 protein
B: BH0493 protein
C: BH0493 protein
J: BH0493 protein
K: BH0493 protein
L: BH0493 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,56040
Polymers305,1676
Non-polymers2,39334
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33210 Å2
ΔGint-115 kcal/mol
Surface area82650 Å2
MethodPISA
6
D: BH0493 protein
E: BH0493 protein
F: BH0493 protein
G: BH0493 protein
H: BH0493 protein
I: BH0493 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,24637
Polymers305,1676
Non-polymers2,08031
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32910 Å2
ΔGint-114 kcal/mol
Surface area81380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)273.720, 158.560, 181.240
Angle α, β, γ (deg.)90.000, 116.030, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131A
141B
151C
161D
171E
181F
191G
201H
211I
221J
231K
241L

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLU5AA0 - 71 - 8
21MSEMSEGLUGLU5BB1 - 72 - 8
31MSEMSEGLUGLU5CC1 - 72 - 8
41GLYGLYGLUGLU5DD0 - 71 - 8
51ILEILEGLUGLU5EE3 - 74 - 8
61SERSERGLUGLU5FF2 - 73 - 8
71MSEMSEGLUGLU5GG1 - 72 - 8
81MSEMSEGLUGLU5HH1 - 72 - 8
91ASNASNGLUGLU5II4 - 75 - 8
101MSEMSEGLUGLU5JJ1 - 72 - 8
111GLYGLYGLUGLU5KK0 - 71 - 8
121SERSERGLUGLU5LL2 - 73 - 8
132VALVALGLYGLY3AA8 - 4139 - 414
142VALVALGLYGLY3BB8 - 4139 - 414
152VALVALGLYGLY3CC8 - 4139 - 414
162VALVALGLYGLY3DD8 - 4139 - 414
172VALVALGLYGLY3EE8 - 4139 - 414
182VALVALGLYGLY3FF8 - 4139 - 414
192VALVALGLYGLY3GG8 - 4139 - 414
202VALVALGLYGLY3HH8 - 4139 - 414
212VALVALGLYGLY3II8 - 4139 - 414
222VALVALGLYGLY3JJ8 - 4139 - 414
232VALVALGLYGLY3KK8 - 4139 - 414
242VALVALGLYGLY3LL8 - 4139 - 414
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TRIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
BH0493 protein


Mass: 50861.109 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans C-125 (bacteria) / Species: Bacillus halodurans / Strain: C-125, DSM 18197, FERM 7344, JCM 9153 / Gene: NP_241359.1, BH0493 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9KFI6

-
Non-polymers , 9 types, 3797 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 3 / Source method: obtained synthetically
#7: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#8: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#9: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3732 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.5 %
Description: THE STRUCTURE WAS SOLVED USING COMBINATION OF MOLECULAR REPLACEMENT (1J5S) AND MULTIPLE-WAVELENGTH ANOMALOUS DISPERSION METHODS. INITIAL HEAVY ATOM SITES WERE OBTAINED USING DIFFERENCE ...Description: THE STRUCTURE WAS SOLVED USING COMBINATION OF MOLECULAR REPLACEMENT (1J5S) AND MULTIPLE-WAVELENGTH ANOMALOUS DISPERSION METHODS. INITIAL HEAVY ATOM SITES WERE OBTAINED USING DIFFERENCE FOURIER WITH MR AND DENSITY MODIFICATION PHASES.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.33
Details: NANODROP, 7.5% PEG 8000, 36.0% 2-methyl-2,4-pentanediol, 0.1M Sodium cacodylate pH 6.33, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97935
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 24, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979351
ReflectionResolution: 2→48.564 Å / Num. obs: 437594 / % possible obs: 93.7 % / Redundancy: 2.83 % / Biso Wilson estimate: 25.43 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2-2.112.580.4422.391288104578672.2
2.11-2.210.3633.21399214634795.9
2.21-2.320.28541319584370297.7
2.32-2.470.2175.11445834862697.9
2.47-2.660.1596.71390884726397.9
2.66-2.930.1099.11411694853598
2.93-3.350.06413.41385644804598.2
3.35-4.210.04118.613883598.2
4.21-48.560.03521.71374374851996.1

-
Phasing

PhasingMethod: MAD/molecular replacement

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
MOLREPphasing
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, MAD
Starting model: PDB entry 1J5S

1j5s


Resolution: 2→48.564 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.732 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.117
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. THREE UNIDENTIFIED DENSITY BLOBS ARE MODELLED AS UNKNOWN LIGANDS (UNL). EACH UNL CONTAINS A HEAVY ATOM (ARSENIC) AND RANDOMLY PLACED OXYGEN ATOMS. 5. GOL, FMT, CL, NA, ACT AND PO4 ARE FROM BUFFER OR CRYSTALLIZATION/CRYO SOLVENT. 6. THE TEST SET FOR FREE-R CALCULATION IS SELECTED BY THIN SHELL METHOD. 7. THE RAMACHANDRAN OUTLIERS IN RESIDUE 41 ARE SUPPORTED BY DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.178 5300 1.2 %THIN SHELLS
Rwork0.148 ---
all0.149 ---
obs0.149 437582 97.54 %-
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: 20.506 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å2-0.89 Å2
2--1.16 Å20 Å2
3----2.35 Å2
Refinement stepCycle: LAST / Resolution: 2→48.564 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41334 0 327 3732 45393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02242999
X-RAY DIFFRACTIONr_bond_other_d0.0020.0229575
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.94358291
X-RAY DIFFRACTIONr_angle_other_deg0.955371668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21555149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08423.9152225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.025157583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8115341
X-RAY DIFFRACTIONr_chiral_restr0.0880.26257
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0247529
X-RAY DIFFRACTIONr_gen_planes_other0.0010.029020
X-RAY DIFFRACTIONr_nbd_refined0.2140.29442
X-RAY DIFFRACTIONr_nbd_other0.1990.232105
X-RAY DIFFRACTIONr_nbtor_refined0.1820.220536
X-RAY DIFFRACTIONr_nbtor_other0.0840.221755
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.23345
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1010.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.219
X-RAY DIFFRACTIONr_mcbond_it1.33325409
X-RAY DIFFRACTIONr_mcbond_other0.495310148
X-RAY DIFFRACTIONr_mcangle_it2.382541224
X-RAY DIFFRACTIONr_scbond_it4.786818425
X-RAY DIFFRACTIONr_scangle_it6.5131117007
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2356TIGHT POSITIONAL0.120.15
2B2356TIGHT POSITIONAL0.130.15
3C2356TIGHT POSITIONAL0.120.15
4D2356TIGHT POSITIONAL0.160.15
5E2356TIGHT POSITIONAL0.120.15
6F2356TIGHT POSITIONAL0.110.15
7G2356TIGHT POSITIONAL0.120.15
8H2356TIGHT POSITIONAL0.140.15
9I2356TIGHT POSITIONAL0.140.15
10J2356TIGHT POSITIONAL0.190.15
11K2356TIGHT POSITIONAL0.140.15
12L2356TIGHT POSITIONAL0.150.15
1A23MEDIUM POSITIONAL0.480.6
2B23MEDIUM POSITIONAL0.710.6
3C23MEDIUM POSITIONAL0.920.6
4D23MEDIUM POSITIONAL0.60.6
5E23MEDIUM POSITIONAL0.730.6
6F23MEDIUM POSITIONAL0.90.6
7G23MEDIUM POSITIONAL0.710.6
8H23MEDIUM POSITIONAL0.720.6
9I23MEDIUM POSITIONAL1.070.6
10J23MEDIUM POSITIONAL0.740.6
11K23MEDIUM POSITIONAL0.440.6
12L23MEDIUM POSITIONAL1.040.6
1A3054LOOSE POSITIONAL0.343
2B3054LOOSE POSITIONAL0.363
3C3054LOOSE POSITIONAL0.333
4D3054LOOSE POSITIONAL0.353
5E3054LOOSE POSITIONAL0.353
6F3054LOOSE POSITIONAL0.43
7G3054LOOSE POSITIONAL0.383
8H3054LOOSE POSITIONAL0.333
9I3054LOOSE POSITIONAL0.383
10J3054LOOSE POSITIONAL0.393
11K3054LOOSE POSITIONAL0.343
12L3054LOOSE POSITIONAL0.353
1A2356TIGHT THERMAL0.491
2B2356TIGHT THERMAL0.421
3C2356TIGHT THERMAL0.431
4D2356TIGHT THERMAL0.391
5E2356TIGHT THERMAL0.361
6F2356TIGHT THERMAL0.381
7G2356TIGHT THERMAL0.541
8H2356TIGHT THERMAL0.541
9I2356TIGHT THERMAL0.481
10J2356TIGHT THERMAL0.541
11K2356TIGHT THERMAL0.541
12L2356TIGHT THERMAL0.631
1A23MEDIUM THERMAL6.615
2B23MEDIUM THERMAL12.425
3C23MEDIUM THERMAL7.345
4D23MEDIUM THERMAL6.015
5E23MEDIUM THERMAL9.365
6F23MEDIUM THERMAL6.935
7G23MEDIUM THERMAL4.365
8H23MEDIUM THERMAL4.025
9I23MEDIUM THERMAL10.185
10J23MEDIUM THERMAL65
11K23MEDIUM THERMAL6.215
12L23MEDIUM THERMAL13.045
1A3054LOOSE THERMAL2.4810
2B3054LOOSE THERMAL2.4910
3C3054LOOSE THERMAL2.3210
4D3054LOOSE THERMAL2.4810
5E3054LOOSE THERMAL2.4210
6F3054LOOSE THERMAL2.4310
7G3054LOOSE THERMAL2.4110
8H3054LOOSE THERMAL2.4310
9I3054LOOSE THERMAL2.4910
10J3054LOOSE THERMAL2.610
11K3054LOOSE THERMAL2.5210
12L3054LOOSE THERMAL2.7610
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.228 22694 -
obs--100 %
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)
10.07980.0513-0.11630.1222-0.01331.3987-0.0198-0.0322-0.0451-0.0525-0.0415-0.03260.21340.17240.0613-0.0130.02390.0223-0.08040.0033-0.041851.163-22.22570.114
20.33720.0557-0.07520.5471-0.37631.22720.0172-0.00310.03190.03610.03850.1134-0.2916-0.4038-0.05570.02840.08380.00610.0528-0.0259-0.039722.234.57273.048
30.3436-0.14510.03090.7168-0.11291.17640.0193-0.00990.0853-0.0302-0.0976-0.1077-0.59780.39070.07830.2161-0.2181-0.01470.02180.0263-0.021559.8215.87476.275
40.68030.04770.04570.3007-0.0011.62610.02370.2067-0.2656-0.1726-0.0733-0.00760.40750.30550.04960.10890.09110.03520.016-0.06840.181553.112-21.545-52.738
51.18010.22140.06870.6665-0.15231.31-0.00320.0869-0.0372-0.078-0.00060.1535-0.2326-0.47360.00380.01140.0536-0.01770.1509-0.02270.060623.4563.995-47.9
60.67850.05070.08330.543-0.24441.45470.00320.09190.0736-0.0388-0.0838-0.0405-0.52070.43370.08070.1631-0.18910.01330.0710.05220.020560.50316.441-46.471
70.2701-0.1231-0.18090.36870.02411.0470.01190.0230.03880.0297-0.0127-0.0276-0.2764-0.15750.0008-0.06030.04210.004-0.13530.0074-0.025438.1988.4639.917
80.35040.06680.03390.4183-0.24891.1211-0.03890.0288-0.04-0.0773-0.0326-0.01770.3904-0.02680.0715-0.0069-0.03010.0543-0.1778-0.0134-0.013446.239-29.9135.817
90.743-0.1994-0.12160.672-0.06860.9072-0.0425-0.02840.03420.0577-0.0827-0.1632-0.05730.4330.1252-0.1507-0.04170.00340.08570.08020.05775.905-3.8567.277
100.21940.01790.05770.24750.09980.9975-0.0140.00480.0525-0.0571-0.04280.0368-0.2824-0.26650.0568-0.06310.0835-0.0232-0.0754-0.0183-0.055633.699.404131.41
110.37550.18550.0040.279-0.03750.74280.0038-0.0101-0.04250.004-0.03-0.04160.247-0.10790.0262-0.0513-0.05810.0061-0.1228-0.0162-0.065241.752-29.331128.22
120.47130.02850.17390.28110.2780.9162-0.00180.1024-0.0269-0.03910.0098-0.0569-0.08680.2441-0.0081-0.1392-0.03750.0133-0.03630.0149-0.050471.111-2.927131.231
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 4231 - 424
22BB1 - 4232 - 424
33CC1 - 4202 - 421
44DD0 - 4131 - 414
55EE3 - 4204 - 421
66FF2 - 4143 - 415
77GG1 - 4232 - 424
88HH1 - 4212 - 422
99II4 - 4235 - 424
1010JJ1 - 4202 - 421
1111KK0 - 4231 - 424
1212LL2 - 4233 - 424

+
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