- PDB-3mbj: Crystal structure of a putative phosphomethylpyrimidine kinase (B... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3mbj
Title
Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution (rhombohedral form)
Components
Putative phosphomethylpyrimidine kinase
Keywords
TRANSFERASE / Putative phosphomethylpyrimidine kinase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Kinase
Function / homology
Function and homology information
pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / phosphorylation / metal ion binding / cytosol Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
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Details
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.
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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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 35.00% 2-methyl-2,4-pentanediol, 0.20M lithium sulfate, 0.1M MES pH 6.0, Additive: 0.001M zinc chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Monochromator: Single crystal Si(111) bent monochromator (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
0.97916
1
3
0.97871
1
Reflection
Resolution: 2.1→29.591 Å / Num. obs: 22278 / % possible obs: 100 % / Redundancy: 5.7 % / Biso Wilson estimate: 28.253 Å2 / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 10.7
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
2.1-2.15
5.7
0.838
0.9
9346
1645
0.838
100
2.15-2.21
5.7
0.703
1.1
8993
1582
0.703
100
2.21-2.28
5.7
0.566
1.2
8763
1537
0.566
100
2.28-2.35
5.7
0.514
1.5
8541
1504
0.514
100
2.35-2.42
5.7
0.432
1.8
8407
1478
0.432
100
2.42-2.51
5.7
0.385
2
8099
1415
0.385
100
2.51-2.6
5.7
0.324
2.3
7698
1351
0.324
100
2.6-2.71
5.7
0.268
2.8
7538
1321
0.268
100
2.71-2.83
5.7
0.231
3.3
7214
1265
0.231
100
2.83-2.97
5.7
0.178
4.2
6893
1209
0.178
100
2.97-3.13
5.7
0.144
5.1
6616
1160
0.144
100
3.13-3.32
5.7
0.115
6.2
6197
1090
0.115
100
3.32-3.55
5.7
0.097
7
5788
1015
0.097
100
3.55-3.83
5.7
0.088
7.3
5454
965
0.088
100
3.83-4.2
5.6
0.079
7.8
4965
884
0.079
100
4.2-4.7
5.6
0.069
8.7
4445
796
0.069
100
4.7-5.42
5.6
0.072
8.5
3986
716
0.072
100
5.42-6.64
5.5
0.079
8.2
3351
605
0.079
100
6.64-9.39
5.4
0.062
9.3
2565
474
0.062
100
9.39-29.59
5.1
0.063
8.7
1355
266
0.063
96.7
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.5.0102
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
autoSHARP
phasing
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.1→29.591 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 9.557 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.154 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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. 4. SULFATE IONS (SO4) AND 2-METHYL-2,4-PENTANEDIOL (MPD & MRD) MOLECULES FROM CRYSTALLIZATION ARE MODELED IN THE STRUCTURE. 5. AN IMIDAZOLE MOLECULE (IMD) FROM THE PROTEIN BUFFER IS MODELED IN THIS STRUCTURE. 6. ZINC IONS (ZN) AND A CHLORIDE ANION (CL) FROM THE CRYSTALLIZATION DROP ADDITIVE ARE MODELED IN THE STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21
1137
5.1 %
RANDOM
Rwork
0.171
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obs
0.173
22278
99.95 %
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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
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