- PDB-4f78: Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4f78
Title
Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg
Components
D,D-dipeptidase/D,D-carboxypeptidase
Keywords
HYDROLASE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / NIAID / ALPHA+BETA PROTEIN / METALLOPEPTIDASE / HEDGEHOG/DD-PEPTIDASE FOLD / MEROPS M15B SUBFAMILY / ZN2+-DEPENDENT D / D-DIPEPTIDASE / VANCOMYCIN RESISTANCE / D-ALANINE-D-ALANINE
Resolution: 1.95→2.06 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2850 / % possible all: 100
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Processing
Software
Name
Version
Classification
HKL-3000
datacollection
PHENIX
(phenix.autosol)
modelbuilding
PHENIX
(phenix.refine: 1.7.3_928)
refinement
XDS
datareduction
SCALA
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.95→39.584 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.5 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1864
949
4.99 %
random
Rwork
0.1536
-
-
-
obs
0.1554
19734
98.35 %
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Solvent computation
Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.654 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
-1.7143 Å2
0 Å2
-4.2779 Å2
2-
-
1.3494 Å2
-0 Å2
3-
-
-
0.3648 Å2
Refinement step
Cycle: LAST / Resolution: 1.95→39.584 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2054
0
65
187
2306
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.016
2201
X-RAY DIFFRACTION
f_angle_d
1.494
2966
X-RAY DIFFRACTION
f_dihedral_angle_d
14.268
840
X-RAY DIFFRACTION
f_chiral_restr
0.116
310
X-RAY DIFFRACTION
f_plane_restr
0.007
386
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.95-2.0027
0.2775
123
0.2171
2747
X-RAY DIFFRACTION
98
2.0027-2.0617
0.2068
146
0.1947
2708
X-RAY DIFFRACTION
98
2.0617-2.1282
0.2173
144
0.1755
2768
X-RAY DIFFRACTION
98
2.1282-2.2043
0.2052
137
0.1596
2715
X-RAY DIFFRACTION
98
2.2043-2.2925
0.2152
146
0.16
2811
X-RAY DIFFRACTION
98
2.2925-2.3968
0.1972
151
0.1557
2673
X-RAY DIFFRACTION
98
2.3968-2.5232
0.2262
151
0.158
2766
X-RAY DIFFRACTION
98
2.5232-2.6812
0.1956
136
0.1529
2757
X-RAY DIFFRACTION
99
2.6812-2.8882
0.1882
152
0.1515
2757
X-RAY DIFFRACTION
99
2.8882-3.1787
0.1934
153
0.1497
2758
X-RAY DIFFRACTION
99
3.1787-3.6384
0.1718
145
0.1439
2772
X-RAY DIFFRACTION
99
3.6384-4.5829
0.1564
147
0.1227
2756
X-RAY DIFFRACTION
99
4.5829-39.5926
0.1556
144
0.1596
2738
X-RAY DIFFRACTION
98
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
0.3823
0.0117
0.5165
0.7702
-0.0827
1.4629
-0.0166
-0.3294
-0.2666
0.1715
0.0401
0.1086
0.1831
-0.0589
-0.0657
0.1352
-0.0144
0.0118
0.1233
0.0325
0.1346
-13.4764
-13.882
-18.1936
2
1.0575
-0.424
-0.5374
1.6291
0.7564
3.0137
0.0413
-0.0201
0.0131
-0.0517
-0.0586
0.0985
0.0093
-0.1347
0.0057
0.0502
-0.0142
-0.0138
0.0542
0.005
0.1032
-17.2558
-5.3482
-31.1827
3
2.6162
-0.66
-0.0608
2.2842
-0.2919
2.1523
0.0153
-0.0502
0.1704
-0.0675
0.0561
0.0946
-0.2049
-0.1041
-0.0282
0.0715
-0.0035
0.0197
0.0411
-0.0185
0.0841
-11.8754
3.1163
-23.7725
4
2.7849
0.4257
0.4265
3.8666
-0.5094
3.098
-0.0539
-0.6402
-0.0715
0.7326
-0.0311
0.0969
0.2433
-0.0655
0.0156
0.1725
0.0405
-0.0385
0.2656
0.0223
0.0305
-3.1852
-8.8349
-5.4101
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chainAandresi0:50
2
X-RAY DIFFRACTION
2
chainAandresi51:116
3
X-RAY DIFFRACTION
3
chainAandresi117:194
4
X-RAY DIFFRACTION
4
chainAandresi195:250
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