- PDB-4ezv: Crystal structure of the substrate binding domain of E.coli DnaK ... -
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Basic information
Entry
Database: PDB / ID: 4ezv
Title
Crystal structure of the substrate binding domain of E.coli DnaK in complex with PR-bombesin in space group P21212
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 / neuropeptide signaling pathway / protein unfolding / cellular response to unfolded protein / inclusion body / protein folding chaperone / heat shock protein binding / ATP-dependent protein folding chaperone ...stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / neuropeptide signaling pathway / protein unfolding / cellular response to unfolded protein / inclusion body / protein folding chaperone / heat shock protein binding / ATP-dependent protein folding chaperone / ADP binding / unfolded protein binding / protein-folding chaperone binding / protein refolding / response to heat / 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.
Resolution: 2.1→2.21 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.471 / % possible all: 100
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Processing
Software
Name
Version
Classification
MAR345
datacollection
MOLREP
phasing
REFMAC
5.6.0117
refinement
XDS
datareduction
SCALA
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.197 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.186 / 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
0.25899
1150
3.1 %
RANDOM
Rwork
0.20957
-
-
-
obs
0.21115
35866
99.72 %
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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: 43.427 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.94 Å2
0 Å2
0 Å2
2-
-
-1.29 Å2
0 Å2
3-
-
-
0.35 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→25 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3491
0
0
146
3637
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.02
3604
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.962
1.961
4876
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.824
5
475
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
41.652
26.386
166
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.448
15
686
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
23.588
15
16
X-RAY DIFFRACTION
r_chiral_restr
0.136
0.2
566
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.021
2682
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: 2.1→2.154 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.326
76
-
Rwork
0.266
2379
-
obs
-
-
99.96 %
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
0.683
1.0438
0.1111
6.0936
2.3284
1.3515
-0.053
0.1013
-0.0935
0.1838
0.2155
-0.2527
0.1516
0.0613
-0.1625
0.1314
-0.0197
-0.0382
0.1332
-0.0412
0.0805
-16.9719
7.3063
-13.244
2
2.2979
0.7798
-0.5286
4.2504
0.1083
1.5121
-0.0226
0.0594
-0.0373
0.2667
0.1952
-0.3246
-0.0861
0.0962
-0.1726
0.0829
0.0009
-0.0412
0.0921
-0.0531
0.0741
-11.7881
20.0334
-9.2197
3
2.4062
2.4666
-1.4544
7.3389
-1.1566
3.2358
-0.2406
0.0264
-0.2837
-0.0768
0.3236
-0.6579
0.5144
0.3449
-0.083
0.1267
0.0545
-0.0586
0.0776
-0.0554
0.1203
-10.2491
10.262
-8.2964
4
0.1874
0.0076
-0.3317
17.9406
-2.0042
1.6506
0.0853
-0.0154
0.0248
0.1239
0.0364
0.1459
-0.1592
-0.0046
-0.1217
0.0837
0.0156
0.0702
0.0877
-0.0036
0.101
-27.523
31.9771
-5.3466
5
2.5807
0.4237
-0.8071
3.958
-0.7288
2.8782
0.106
-0.1292
0.2011
0.0934
-0.0945
0.022
-0.3009
-0.0403
-0.0115
0.1926
0.0632
0.079
0.094
-0.0384
0.1036
-32.0598
43.1845
-5.2423
6
7.7684
15.9065
-11.2043
32.5917
-22.9513
16.1721
-0.4112
0.3933
0.5774
-1.2067
1.0317
1.185
0.8704
-0.5761
-0.6205
0.6173
-0.0116
0.1214
0.4259
0.1859
0.5975
-51.1791
2.7421
-11.0377
7
0.7997
0.3623
0.0066
3.473
1.0862
1.4722
-0.0706
-0.0293
0.0659
0.0392
0.1381
0.2349
-0.0063
-0.1288
-0.0675
0.0417
0.0465
0.0057
0.1079
0.0692
0.0849
-41.524
24.1659
-20.326
8
3.8758
6.3246
0.622
10.4191
0.9863
1.0631
0.1078
-0.0738
-0.0915
0.079
-0.1568
-0.1262
-0.0048
0.043
0.049
0.1056
0.0107
0.0073
0.1267
0.0191
0.1463
-24.1975
23.6903
-25.3305
9
2.6133
1.5385
-0.7015
5.5757
0.0804
3.4124
0.0144
0.1049
0.0013
-0.1772
0.1231
-0.3104
-0.1802
0.0482
-0.1375
0.0999
-0.0333
0.0594
0.1282
0.0711
0.1191
-11.7194
37.1378
-28.071
10
3.5897
3.7206
0.4699
20.0896
9.9063
16.781
0.3154
-0.9977
-0.0659
1.8182
0.0232
-1.2785
0.5892
0.4182
-0.3386
0.4121
-0.0893
-0.091
0.5135
-0.0416
0.2201
-7.5706
44.0596
-15.2834
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
389 - 421
2
X-RAY DIFFRACTION
2
A
422 - 484
3
X-RAY DIFFRACTION
3
A
485 - 517
4
X-RAY DIFFRACTION
4
A
518 - 558
5
X-RAY DIFFRACTION
5
A
559 - 607
6
X-RAY DIFFRACTION
6
B
389 - 394
7
X-RAY DIFFRACTION
7
B
395 - 512
8
X-RAY DIFFRACTION
8
B
513 - 552
9
X-RAY DIFFRACTION
9
B
553 - 594
10
X-RAY DIFFRACTION
10
B
595 - 604
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