- PDB-4ezu: Crystal structure of the substrate binding domain of E.coli DnaK ... -
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Basic information
Entry
Database: PDB / ID: 4ezu
Title
Crystal structure of the substrate binding domain of E.coli DnaK in complex with PR-bombesin in space group I222
Components
Chaperone protein DnaK
Proline rich bombesin-related protein
Keywords
CHAPERONE/PEPTIDE BINDING PROTEIN / chaperone / peptide binding / CHAPERONE-PEPTIDE BINDING PROTEIN complex
Function / homology
Function and homology information
stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / neuropeptide signaling pathway / cellular response to unfolded protein / protein folding chaperone / inclusion body / heat shock protein binding / ATP-dependent protein folding chaperone ...stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / neuropeptide signaling pathway / cellular response to unfolded protein / protein folding chaperone / inclusion body / heat shock protein binding / ATP-dependent protein folding chaperone / ADP binding / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / protein-containing complex assembly / DNA replication / ATP hydrolysis activity / protein-containing complex / zinc ion binding / extracellular region / ATP binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function
Bombesin/neuromedin-B/ranatensin peptide family / Bombesin-like peptide / Bombesin-like peptides family signature. / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. ...Bombesin/neuromedin-B/ranatensin peptide family / Bombesin-like peptide / Bombesin-like peptides family signature. / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Chaperone DnaK / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / ATPase, nucleotide binding domain / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha Similarity search - Domain/homology
Journal: To be Published Title: Structural studies of DnaK in complex with proline rich antimicrobial peptides reveal two different peptide binding modes Authors: Zahn, M. / Straeter, N.
Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2010
Radiation
Monochromator: Si - 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.91841 Å / Relative weight: 1
Reflection
Resolution: 1.9→25 Å / Num. obs: 17741 / % possible obs: 99.8 % / Rmerge(I) obs: 0.062
Reflection shell
Resolution: 1.9→2 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.558 / % possible all: 100
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Processing
Software
Name
Version
Classification
MAR345
datacollection
REFMAC
withPDBID1DKZ
refinement
XDS
datareduction
SCALA
datascaling
REFMAC
withPDBID1DKZ
phasing
Refinement
Method to determine structure: PDB ID 1DKZ / Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 9.73 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27582
901
5.1 %
RANDOM
Rwork
0.21776
-
-
-
obs
0.22064
16807
99.57 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 35.847 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.88 Å2
0 Å2
0 Å2
2-
-
-2.14 Å2
0 Å2
3-
-
-
3.02 Å2
Refinement step
Cycle: LAST / Resolution: 1.9→25 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1749
0
0
80
1829
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.02
1795
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.931
1.966
2429
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.227
5
235
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
42.028
26.463
82
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.106
15
338
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.033
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.129
0.2
283
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.021
1335
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.9→1.949 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.383
55
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Rwork
0.272
1136
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obs
-
-
99.92 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°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)
1
0.6729
1.5744
0.9985
4.004
1.8062
2.4099
-0.0039
0.0424
-0.0111
-0.0035
0.0599
-0.0227
0.0523
0.0763
-0.0559
0.1502
0.0189
-0.0059
0.186
-0.0079
0.1382
62.5408
103.7951
38.1547
2
0.9589
-0.0549
0.5582
2.4311
-0.3189
1.1538
0.0533
0.0803
-0.2467
-0.2343
0.0744
-0.1019
0.107
0.0036
-0.1277
0.1538
0.0321
-0.0097
0.1397
-0.0041
0.1227
63.3594
90.5099
33.9227
3
2.3472
0.5126
-0.1734
5.4959
-1.1431
0.8878
-0.0905
0.2373
0.0056
-0.042
0.0325
0.0366
-0.0826
0.1262
0.058
0.1634
0.028
0.0172
0.1474
-0.0274
0.0505
61.3453
101.1881
30.3181
4
3.6556
2.8366
0.6523
11.3781
-1.1225
2.3661
0.2292
-0.0191
-0.2265
0.048
-0.1052
-0.4346
0.3095
0.0573
-0.124
0.1396
-0.0122
-0.0935
0.0862
-0.0163
0.1698
42.8047
74.7923
29.5546
5
5.003
-1.6968
0.4264
3.8476
-3.3948
4.9932
0.2401
0.1685
-0.169
-0.2762
0.0904
0.2326
0.3009
-0.0659
-0.3306
0.1583
-0.0766
-0.1393
0.1134
0.0183
0.1798
37.8018
77.1077
27.5935
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
389 - 423
2
X-RAY DIFFRACTION
2
A
424 - 488
3
X-RAY DIFFRACTION
3
A
489 - 529
4
X-RAY DIFFRACTION
4
A
530 - 564
5
X-RAY DIFFRACTION
5
A
565 - 604
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