- PDB-2qjw: CRYSTAL STRUCTURE OF A PUTATIVE HYDROLASE OF THE ALPHA/BETA SUPER... -
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Basic information
Entry
Database: PDB / ID: 2qjw
Title
CRYSTAL STRUCTURE OF A PUTATIVE HYDROLASE OF THE ALPHA/BETA SUPERFAMILY (XCC1541) FROM XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS AT 1.35 A RESOLUTION
Components
Uncharacterized protein XCC1541
Keywords
HYDROLASE / PUTATIVE HYDROLASE OF THE ALPHA/BETA SUPERFAMILY / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF FOUR ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF FOUR CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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.
#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)
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Assembly
Deposited unit
A: Uncharacterized protein XCC1541 B: Uncharacterized protein XCC1541 C: Uncharacterized protein XCC1541 D: Uncharacterized protein XCC1541 hetero molecules
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 3, 2007 / Details: Flat mirror (vertical focusing)
Radiation
Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.9792
1
Reflection
Resolution: 1.35→29.775 Å / Num. obs: 140150 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.984 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 10.76
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
1.35-1.4
0.508
1.5
45721
26866
93.9
1.4-1.45
0.446
1.7
41303
23723
95.8
1.45-1.52
0.364
2.1
49381
28433
96.4
1.52-1.6
0.277
2.8
46539
26766
96.7
1.6-1.7
0.206
3.7
46700
26895
97.5
1.7-1.83
0.143
5.4
46766
26927
98.2
1.83-2.02
0.084
9.1
48622
28129
98.7
2.02-2.31
0.046
15.5
46772
27065
99
2.31-2.91
0.029
23.6
48274
27417
99.3
2.91-29.775
0.015
40.8
48860
27217
98.6
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3
dataextraction
MAR345
CCD
datacollection
XDS
datareduction
SHELXD
phasing
SOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.35→29.775 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.211 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.064 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. CHLORIDE IONS, TARTRATE ION AND THE FRAGMENTS OF POLYETHYLENE GLYCOL 400 MOLECULE WITH DIFFERENT MOLECULAR WEIGHT WERE MODELED IN THIS STRUCTURE. 4. RESIDUES 71 TO 75 IN SUBUNIT D ARE DISORDERED AND NOT MODELED IN THE STRUCTURE. 5. UNEXPLAINED ELECTRON DENSITY NEAR RESIDUES A147 AND D147 ARE NOT MODELED. THEY ARE SUGGESTED AS NITROBENZENE (NBZ).
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.216
7030
5 %
RANDOM
Rwork
0.182
-
-
-
obs
0.184
140130
99.67 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 12.979 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.8 Å2
0 Å2
0.26 Å2
2-
-
0.47 Å2
0 Å2
3-
-
-
0.37 Å2
Refinement step
Cycle: LAST / Resolution: 1.35→29.775 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5138
0
65
767
5970
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.021
5564
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.02
3709
X-RAY DIFFRACTION
r_angle_refined_deg
1.767
1.976
7605
X-RAY DIFFRACTION
r_angle_other_deg
1.124
3
9049
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.251
5
748
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
26.402
22.44
209
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.019
15
859
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.9
15
49
X-RAY DIFFRACTION
r_chiral_restr
0.075
0.2
881
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
6378
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
1116
X-RAY DIFFRACTION
r_nbd_refined
0.221
0.3
1266
X-RAY DIFFRACTION
r_nbd_other
0.193
0.3
4240
X-RAY DIFFRACTION
r_nbtor_refined
0.175
0.5
2805
X-RAY DIFFRACTION
r_nbtor_other
0.092
0.5
2926
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.183
0.5
967
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.115
0.3
25
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.283
0.3
124
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.224
0.5
78
X-RAY DIFFRACTION
r_mcbond_it
1.906
3
3716
X-RAY DIFFRACTION
r_mcbond_other
0.926
3
1460
X-RAY DIFFRACTION
r_mcangle_it
2.615
5
5817
X-RAY DIFFRACTION
r_scbond_it
3.989
8
2039
X-RAY DIFFRACTION
r_scangle_it
5.57
11
1788
Refine LS restraints NCS
Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
Dom-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
A
908
MEDIUMPOSITIONAL
0.27
0.5
2
B
908
MEDIUMPOSITIONAL
0.29
0.5
3
C
908
MEDIUMPOSITIONAL
0.22
0.5
4
D
908
MEDIUMPOSITIONAL
0.21
0.5
1
A
911
LOOSEPOSITIONAL
0.46
5
2
B
911
LOOSEPOSITIONAL
0.49
5
3
C
911
LOOSEPOSITIONAL
0.45
5
4
D
911
LOOSEPOSITIONAL
0.37
5
1
A
908
MEDIUMTHERMAL
1.84
2
2
B
908
MEDIUMTHERMAL
1.35
2
3
C
908
MEDIUMTHERMAL
1.65
2
4
D
908
MEDIUMTHERMAL
1.85
2
1
A
911
LOOSETHERMAL
2.41
10
2
B
911
LOOSETHERMAL
1.92
10
3
C
911
LOOSETHERMAL
2.18
10
4
D
911
LOOSETHERMAL
2.31
10
LS refinement shell
Resolution: 1.35→1.384 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.368
534
-
Rwork
0.337
9712
-
obs
-
10246
98.6 %
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