- PDB-1vkz: Crystal structure of Phosphoribosylamine--glycine ligase (TM1250)... -
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Basic information
Entry
Database: PDB / ID: 1vkz
Title
Crystal structure of Phosphoribosylamine--glycine ligase (TM1250) from Thermotoga maritima at 2.30 A resolution
Components
Phosphoribosylamine--glycine ligase
Keywords
LIGASE / TM1250 / PHOSPHORIBOSYLAMINE--GLYCINE LIGASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information
phosphoribosylamine-glycine ligase / phosphoribosylamine-glycine ligase activity / purine nucleobase biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 2
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Sample preparation
Crystal
ID
Density Matthews (Å3/Da)
Density % sol (%)
Description
1
2.29
46.21
2
2.44
49.26
TWO CRYSTALS WERE USED IN THE SOLUTION OF THE STRUCTURE. ONE CRYSTAL WAS USED FOR SE-MET MAD PHASING AND ANOTHER WAS USED FOR PHASE EXTENSION AND REFINEMENT.
water cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Radiation
ID
Monochromator
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
DoubleCrystalSi(111)
SINGLEWAVELENGTH
M
x-ray
1
2
Rosenbaum-Rock double-crystal monochromator
MAD
M
x-ray
2
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1
1
2
0.979127
1
3
0.979292
1
4
0.964063
1
Reflection
Resolution: 2.3→37.4 Å / Num. obs: 31749 / % possible obs: 85.6 % / Redundancy: 2 % / Biso Wilson estimate: 54.3 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.1
Reflection shell
Resolution: 2.3→2.36 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 1.3 / Num. unique all: 2434 / % possible all: 88.2
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Processing
Software
Name
Version
Classification
DENZO
datareduction
SCALA
4.2)
datascaling
SOLVE
phasing
REFMAC
5.2.0000
refinement
CCP4
(SCALA)
datascaling
Refinement
Method to determine structure: MAD / Resolution: 2.3→37.26 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 20.438 / SU ML: 0.232 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.591 / ESU R Free: 0.299 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PHASES USED FOR THE RESTRAINTS WERE DENSITY MODIFIED (SOLVENT FLATTENED, HISTOGRAM, MULTI RESOLUTION) PHASES EXTENDED FROM STARTING MAD ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PHASES USED FOR THE RESTRAINTS WERE DENSITY MODIFIED (SOLVENT FLATTENED, HISTOGRAM, MULTI RESOLUTION) PHASES EXTENDED FROM STARTING MAD PHASES FROM A DIFFERENT CRYSTAL. THE FOLLOWING RESIDUES HAVE UNMODELED ATOMS DUE TO MISSING DENSITY: A141 A151 A156 A303 A340 A374 A378 B54 B86 B141 B151 B303. NO DENSITY WAS PRESENT FOR THE LOOP EXTENDING FROM RESIDUES 73 TO 77.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26383
1560
5 %
RANDOM
Rwork
0.21315
-
-
-
obs
0.21572
29714
84.01 %
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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: 44.622 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.3 Å2
0 Å2
-0.69 Å2
2-
-
2.77 Å2
0 Å2
3-
-
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-3.19 Å2
Refinement step
Cycle: LAST / Resolution: 2.3→37.26 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6065
0
4
121
6190
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
6198
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
5742
X-RAY DIFFRACTION
r_angle_refined_deg
1.491
1.966
8355
X-RAY DIFFRACTION
r_angle_other_deg
0.811
3
13357
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.293
5
778
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.517
23.723
274
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.106
15
1078
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.757
15
43
X-RAY DIFFRACTION
r_chiral_restr
0.083
0.2
890
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
6921
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1264
X-RAY DIFFRACTION
r_nbd_refined
0.207
0.2
1337
X-RAY DIFFRACTION
r_nbd_other
0.183
0.2
6078
X-RAY DIFFRACTION
r_nbtor_other
0.089
0.2
4016
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.177
0.2
224
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.181
0.2
20
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.22
0.2
59
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.143
0.2
8
X-RAY DIFFRACTION
r_mcbond_it
1.937
3
4146
X-RAY DIFFRACTION
r_mcbond_other
0.479
3
1624
X-RAY DIFFRACTION
r_mcangle_it
2.76
5
6161
X-RAY DIFFRACTION
r_scbond_it
5.184
8
2578
X-RAY DIFFRACTION
r_scangle_it
7.017
11
2194
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.057
0.2
1
Refine LS restraints NCS
Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
Ens-ID
Number
Type
Rms dev position (Å)
Weight position
1
415
tightpositional
0.03
0.05
1
670
mediumpositional
0.32
0.5
1
415
tightthermal
0.09
0.5
1
670
mediumthermal
0.51
2
2
575
tightpositional
0.03
0.05
2
967
mediumpositional
0.24
0.5
2
575
tightthermal
0.14
0.5
2
967
mediumthermal
0.7
2
3
650
tightpositional
0.03
0.05
3
998
mediumpositional
0.36
0.5
3
650
tightthermal
0.12
0.5
3
998
mediumthermal
0.65
2
4
635
tightpositional
0.04
0.05
4
966
mediumpositional
0.36
0.5
4
635
tightthermal
0.12
0.5
4
966
mediumthermal
0.69
2
LS refinement shell
Resolution: 2.3→2.36 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.405
103
4.32 %
Rwork
0.313
2280
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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
3.1618
0.3203
0.6558
2.1463
0.4236
5.7462
-0.0423
-0.1412
-0.039
0.1377
0.0056
-0.1407
0.1864
0.4482
0.0367
-0.1605
0.119
-0.0538
-0.1037
0.0196
-0.0821
33.222
38.682
52.143
2
4.175
-1.1398
-1.5841
3.3505
1.1251
4.2424
0.18
-0.1875
0.1188
0.2294
0.0085
0.1371
-0.1458
-0.3422
-0.1885
-0.1218
-0.0295
0.0011
-0.1121
0.0636
-0.1156
9.168
43.794
48.707
3
3.9792
-0.6847
0.3593
3.0953
-0.4586
3.5879
-0.0723
0.1013
0.0577
-0.0117
0.0539
0.0768
0.0032
-0.2871
0.0184
-0.2444
-0.0501
0.0003
-0.1479
-0.0112
-0.1024
-9.226
38.707
89.239
4
4.0923
1.1651
-1.1394
4.4822
-0.3782
3.0982
0.1093
0.287
0.2771
-0.3424
0.1249
-0.1303
-0.3777
0.2979
-0.2341
-0.1213
-0.0144
0.0368
-0.1264
-0.0443
-0.1191
14.959
43.717
93.056
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
4 - 83
16 - 95
2
1
A
A
200 - 227
212 - 239
3
1
A
A
278 - 399
290 - 411
4
2
A
A
84 - 199
96 - 211
5
2
A
A
228 - 277
240 - 289
6
3
B
B
4 - 83
16 - 95
7
3
B
B
200 - 227
212 - 239
8
3
B
B
278 - 399
290 - 411
9
4
B
B
84 - 199
96 - 211
10
4
B
B
228 - 277
240 - 289
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