- PDB-2y7g: Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme ... -
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Basic information
Entry
Database: PDB / ID: 2y7g
Title
Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (Kce) from C. Cloacamonas acidaminovorans in complex with the product acetoacetate
Components
3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME
Keywords
LYASE / ALDOLASE
Function / homology
Function and homology information
3-keto-5-aminohexanoate cleavage enzyme / 3-keto-5-aminohexanoate cleavage activity / L-lysine catabolic process to acetate / metal ion binding Similarity search - Function
3-keto-5-aminohexanoate cleavage enzyme / beta-keto acid cleavage enzyme / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta Similarity search - Domain/homology
SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.
Resolution: 1.4→28 Å / Cor.coef. Fo:Fc: 0.9617 / Cor.coef. Fo:Fc free: 0.9462 / SU R Cruickshank DPI: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.058 / SU Rfree Blow DPI: 0.057 / SU Rfree Cruickshank DPI: 0.056 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN AAE MG GOL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4736. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN AAE MG GOL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4736. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=20. NUMBER TREATED BY BAD NON- BONDED CONTACTS=4.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1863
5254
5.06 %
RANDOM
Rwork
0.1666
-
-
-
obs
0.1676
103836
99.18 %
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Displacement parameters
Biso mean: 20.91 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.3491 Å2
0 Å2
0 Å2
2-
-
0.3491 Å2
0 Å2
3-
-
-
-0.6981 Å2
Refine analyze
Luzzati coordinate error obs: 0.157 Å
Refinement step
Cycle: LAST / Resolution: 1.4→28 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4223
0
24
498
4745
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
4343
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.06
5900
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
2018
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
107
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
640
HARMONIC
5
X-RAY DIFFRACTION
t_it
4331
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
2
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_omega_torsion
4.68
X-RAY DIFFRACTION
t_other_torsion
2.61
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
599
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
3
HARMONIC
1
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
5497
SEMIHARMONIC
4
LS refinement shell
Resolution: 1.4→1.44 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.2128
382
5.09 %
Rwork
0.196
7125
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all
0.1968
7507
-
obs
-
-
99.18 %
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
1.5209
-0.3552
0.1175
0.4663
0.1148
0.8367
-0.1176
-0.0042
0.1722
-0.1646
0.031
0.0309
-0.2195
0.0288
0.0867
0.0219
-0.0613
-0.0186
-0.0596
0.0213
-0.0119
-0.7093
38.0831
20.5791
2
0
1.4575
-1.6589
2.5162
-0.8163
0.3215
-0.0101
0.1052
0.036
-0.0056
-0.0181
-0.0907
0.0024
-0.0521
0.0281
0.0222
-0.0715
-0.04
0.0128
0.0743
0.0307
3.8264
38.6145
10.6147
3
0.5657
-0.0224
0.1445
0.5191
-0.0292
0.4666
-0.0294
0.0886
0.0754
-0.0934
-0.0421
-0.0131
-0.0966
-0.0002
0.0715
0.0075
-0.0155
-0.0199
-0.0201
0.0044
-0.0352
-11.8459
22.6486
15.8926
4
0.2861
-0.064
0.1531
0.4229
0.2398
0.3711
0.002
-0.0037
0.0513
-0.0634
0.0178
-0.1206
-0.013
0.0396
-0.0198
-0.0152
-0.0421
0.0097
-0.0039
0.0055
0.002
5.7259
23.5608
24.8936
5
0.3339
-0.5843
-0.3823
1.9403
1.5519
1.9896
0.0054
0.3501
-0.0916
-0.2803
-0.1349
-0.0814
-0.16
0.0584
0.1295
0.037
-0.0564
0.0288
0.0556
0.0273
-0.0337
5.9255
25.8751
5.61
6
0.5962
-0.411
0.6438
1.5474
-0.3347
0.5423
-0.0711
-0.019
0.1811
0.0031
-0.0046
-0.3645
0.0122
0.2108
0.0757
-0.0958
-0.0007
0.0212
0.0205
0.0204
0.029
32.4671
2.8289
34.5191
7
1.3048
-0.5553
0.6034
1.5854
-0.0576
0.1596
-0.0903
-0.0509
0.1959
0.2021
0.1161
-0.2677
0.0467
0.1239
-0.0258
-0.0417
0.0165
-0.0148
0.0381
-0.0041
0.0248
30.7782
0.1591
40.6234
8
0.7786
0.009
0.4689
0.5239
-0.1542
0.6815
0.0341
-0.0285
-0.0593
0.0004
-0.03
-0.0857
0.0943
0.0828
-0.0042
-0.0235
0.0324
0.0097
0.0127
0.0225
-0.0356
20.3737
-11.5438
37.0929
9
1.0258
-0.1765
0.5617
0.609
-0.1776
0.187
-0.0231
-0.0976
-0.0279
0.0412
0.014
-0.0137
0.034
0.0391
0.0092
-0.0042
0.014
0.0158
0.0094
0.0127
-0.0234
8.6962
-3.7434
34.3917
10
0.4937
-0.0594
0.0173
1.1037
-0.2528
0.6393
-0.1031
0.003
0.1262
-0.0148
0.0431
-0.1564
-0.0183
0.0809
0.06
-0.0479
-0.0145
0.0024
0.0164
-0.0034
0.0133
19.5072
10.2433
31.8313
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(A0 - A68 )
2
X-RAY DIFFRACTION
2
(A69 - A80 )
3
X-RAY DIFFRACTION
3
(A81 - A195 )
4
X-RAY DIFFRACTION
4
(A196 - A262 )
5
X-RAY DIFFRACTION
5
(A263 - A275 )
6
X-RAY DIFFRACTION
6
(B0 - B68 )
7
X-RAY DIFFRACTION
7
(B69 - B89 )
8
X-RAY DIFFRACTION
8
(B90 - B154 )
9
X-RAY DIFFRACTION
9
(B155 - B198 )
10
X-RAY DIFFRACTION
10
(B199 - B275 )
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