- PDB-3dl1: Crystal structure of a Putative Metal-dependent Hydrolase (YP_001... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3dl1
Title
Crystal structure of a Putative Metal-dependent Hydrolase (YP_001336084.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.20 A resolution
Components
Putative Metal-dependent Hydrolase
Keywords
HYDROLASE / YP_001336084.1 / A Putative Metal-dependent Hydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Protein of unknown function (DUF980) / unknown function
Function / homology
Function and homology information
Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding / cytosol Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE TARGET PROTEIN SEQUENCE MATCHES TO GENBANK ENTRY YP_001336084.1.YP_001336084.1, COMPARED TO UNP MATCH A6TB83, HAS AN EXTRA RESIDEU MET AT THE BEGINNING OF THE SEQUENCE.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.0000M (NH4)2HPO4, 0.2000M NaCl, 0.1M Imidazole pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 16, 2008 / Details: Flat mirror (vertical focusing)
Radiation
Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Relative weight: 1
Reflection
Resolution: 2.2→29.311 Å / Num. obs: 17061 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 5.9
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.2-2.26
7.3
0.678
1.1
8841
1212
0.678
100
2.26-2.32
7.3
0.458
1.6
8965
1230
0.458
100
2.32-2.39
7.2
0.413
1.8
8345
1152
0.413
100
2.39-2.46
7.4
0.322
2.3
8366
1133
0.322
100
2.46-2.54
7.2
0.29
2.6
7954
1104
0.29
100
2.54-2.63
7.3
0.221
3.4
7921
1079
0.221
100
2.63-2.73
7.2
0.186
3.9
7439
1035
0.186
100
2.73-2.84
7.3
0.141
5.2
7428
1014
0.141
100
2.84-2.97
7.2
0.118
6.1
6802
948
0.118
100
2.97-3.11
7.3
0.097
7.2
6768
931
0.097
100
3.11-3.28
7.2
0.089
7.5
6192
865
0.089
100
3.28-3.48
7.2
0.078
8.3
5956
833
0.078
100
3.48-3.72
7.1
0.073
8.5
5699
802
0.073
100
3.72-4.02
7
0.071
8.5
5179
740
0.071
100
4.02-4.4
7
0.058
10
4783
687
0.058
100
4.4-4.92
6.9
0.053
11.3
4319
622
0.053
100
4.92-5.68
6.8
0.057
9.9
3855
568
0.057
100
5.68-6.96
6.5
0.064
9.5
3147
482
0.064
100
6.96-9.84
6.3
0.052
11
2503
395
0.052
100
9.84-29.31
5.3
0.047
13.3
1220
229
0.047
95.2
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
3.004
dataextraction
MOSFLM
datareduction
SHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.2→29.311 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 8.619 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.15 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.202
861
5.1 %
RANDOM
Rwork
0.171
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-
-
obs
0.172
16997
99.74 %
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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: 37.533 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.14 Å2
0 Å2
0 Å2
2-
-
1.14 Å2
0 Å2
3-
-
-
-2.29 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→29.311 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1664
0
1
97
1762
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
1731
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1147
X-RAY DIFFRACTION
r_angle_refined_deg
1.375
1.946
2366
X-RAY DIFFRACTION
r_angle_other_deg
0.928
3
2787
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.983
5
213
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.303
23.571
84
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.22
15
263
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.88
15
11
X-RAY DIFFRACTION
r_chiral_restr
0.089
0.2
262
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
1936
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
366
X-RAY DIFFRACTION
r_nbd_refined
0.209
0.2
337
X-RAY DIFFRACTION
r_nbd_other
0.183
0.2
1146
X-RAY DIFFRACTION
r_nbtor_refined
0.178
0.2
825
X-RAY DIFFRACTION
r_nbtor_other
0.087
0.2
852
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.159
0.2
67
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.185
0.2
6
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.335
0.2
15
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.079
0.2
5
X-RAY DIFFRACTION
r_mcbond_it
2.144
3
1154
X-RAY DIFFRACTION
r_mcbond_other
0.464
3
416
X-RAY DIFFRACTION
r_mcangle_it
3.215
5
1704
X-RAY DIFFRACTION
r_scbond_it
5.566
8
737
X-RAY DIFFRACTION
r_scangle_it
7.315
11
659
LS refinement shell
Resolution: 2.2→2.257 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.31
61
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Rwork
0.241
1144
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all
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1205
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obs
-
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99.34 %
Refinement TLS params.
Method: refined / Origin x: 50.6167 Å / Origin y: 23.6789 Å / Origin z: 8.5781 Å
11
12
13
21
22
23
31
32
33
T
-0.0905 Å2
0.0668 Å2
0.0467 Å2
-
-0.0374 Å2
0.0732 Å2
-
-
-0.116 Å2
L
2.549 °2
0.4932 °2
0.1559 °2
-
1.4419 °2
0.1114 °2
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-
1.4342 °2
S
0.0746 Å °
-0.2828 Å °
-0.2943 Å °
-0.0665 Å °
-0.0556 Å °
-0.0929 Å °
0.0447 Å °
0.1371 Å °
-0.0189 Å °
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