- PDB-1vkh: CRYSTAL STRUCTURE OF A PUTATIVE SERINE HYDROLASE (YDR428C) FROM S... -
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Basic information
Entry
Database: PDB / ID: 1vkh
Title
CRYSTAL STRUCTURE OF A PUTATIVE SERINE HYDROLASE (YDR428C) FROM SACCHAROMYCES CEREVISIAE AT 1.85 A RESOLUTION
Components
putative serine hydrolase
Keywords
HYDROLASE / PUTATIVE SERINE HYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information
arylformamidase / arylformamidase activity / tryptophan catabolic process to kynurenine / 'de novo' NAD biosynthetic process from tryptophan / NAD biosynthetic process / positive regulation of cell growth / hydrolase activity Similarity search - Function
SEQUENCE CLONING ARTIFACT. THE CONSTRUCT WAS PCR AMPLIFIED WITH TAQ POLYMERASE. SEQUENCING OF THE ...SEQUENCE CLONING ARTIFACT. THE CONSTRUCT WAS PCR AMPLIFIED WITH TAQ POLYMERASE. SEQUENCING OF THE CLONED CONSTRUCT INDICATED THAT VAL IN POSITION 161 WAS MUTATED TO ILE.
Resolution: 1.85→50 Å / Num. obs: 42225 / % possible obs: 99.77 % / Redundancy: 3.89 % / Biso Wilson estimate: 27.53 Å2 / Rsym value: 0.069 / Net I/σ(I): 17.88
Reflection shell
Resolution: 1.85→1.92 Å / Redundancy: 3.57 % / Mean I/σ(I) obs: 3.57 / Num. unique all: 4159 / Rsym value: 0.343 / % possible all: 98.39
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Processing
Software
Name
Version
Classification
DENZO
datareduction
SCALEPACK
datascaling
SOLVE
phasing
RESOLVE
modelbuilding
REFMAC
5.1.9999
refinement
RESOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.85→37.44 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.233 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. NON-ROTOMERS: LEU 156 AND LEU 160 (MOLECULE A AND B).
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1894
2060
5 %
RANDOM
Rwork
0.14292
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-
-
obs
0.14523
39479
100 %
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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: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 26.642 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.07 Å2
0 Å2
-0.02 Å2
2-
-
0.07 Å2
0 Å2
3-
-
-
-0.01 Å2
Refinement step
Cycle: LAST / Resolution: 1.85→37.44 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4133
0
13
454
4600
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.02
0.022
4282
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.02
3868
X-RAY DIFFRACTION
r_angle_refined_deg
1.698
1.955
5801
X-RAY DIFFRACTION
r_angle_other_deg
0.909
3
9055
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.771
5
505
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
40.422
25.271
203
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.328
15
782
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.53
15
16
X-RAY DIFFRACTION
r_chiral_restr
0.11
0.2
669
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
4625
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
811
X-RAY DIFFRACTION
r_nbd_refined
0.215
0.2
955
X-RAY DIFFRACTION
r_nbd_other
0.181
0.2
4037
X-RAY DIFFRACTION
r_nbtor_other
0.088
0.2
2356
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.17
0.2
424
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.245
0.2
26
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.266
0.2
71
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.237
0.2
31
X-RAY DIFFRACTION
r_mcbond_it
1.496
1.5
2801
X-RAY DIFFRACTION
r_mcbond_other
0.373
1.5
1030
X-RAY DIFFRACTION
r_mcangle_it
1.659
2
4214
X-RAY DIFFRACTION
r_scbond_it
3.072
3
1876
X-RAY DIFFRACTION
r_scangle_it
4.247
4.5
1587
LS refinement shell
Resolution: 1.852→1.9 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.264
127
4.92 %
Rwork
0.174
2453
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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
0.672
0.1523
-0.0172
0.5367
-0.0587
1.179
-0.0142
-0.0893
-0.0363
0.0354
-0.0006
-0.0654
0.0542
-0.0167
0.0147
-0.1074
-0.001
0.0052
-0.2667
-0.0023
-0.2105
-8.685
31.714
73.862
2
0.9365
0.0487
0.0372
0.8011
0.1341
1.7341
0.0503
0.131
-0.0146
-0.0491
0.0193
-0.0483
-0.0038
-0.0144
-0.0696
-0.1262
-0.0111
0.013
-0.2414
0.0089
-0.2004
5.075
37.61
41.835
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: ALL
ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
1
A
A
7 - 261
19 - 273
2
2
B
B
10 - 261
22 - 273
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