- PDB-4mjg: Crystal structure of a DUF4853 family protein (ACTODO_00621) from... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4mjg
Title
Crystal structure of a DUF4853 family protein (ACTODO_00621) from Actinomyces odontolyticus ATCC 17982 at 2.65 A resolution
Components
hypothetical protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF16145 family / DUF4853 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / STRUCTURAL GENOMICS UNKNOWN FUNCTION
Function / homology
TBP-like - #30 / Protein of unknown function DUF4853 / Domain of unknown function (DUF4853) / TBP-like / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological species
Actinomyces odontolyticus (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å
Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 29-226 OF 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: 3.32 Å3/Da / Density % sol: 62.94 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2.4M ammonium sulfate, 0.1M Bicine pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2013 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
Radiation
Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.97941
1
3
0.97868
1
Reflection
Resolution: 2.65→44.544 Å / Num. all: 15164 / Num. obs: 15164 / % possible obs: 88.9 % / Redundancy: 3.2 % / Rsym value: 0.061 / Net I/σ(I): 9.2
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
2.65-2.72
3.2
0.811
0.9
3833
1182
0.811
95.3
2.72-2.79
3.2
0.531
1.4
3581
1107
0.531
91.4
2.79-2.87
3.1
0.425
1.7
3007
966
0.425
83.5
2.87-2.96
3.2
0.316
2.3
3416
1068
0.316
93.1
2.96-3.06
3.3
0.244
3
3547
1090
0.244
97.1
3.06-3.17
3.3
0.19
3.9
3372
1024
0.19
96.1
3.17-3.29
3.1
0.139
5.3
3092
986
0.139
95.2
3.29-3.42
3.2
0.106
6.7
2930
923
0.106
91.2
3.42-3.57
3.2
0.078
8.9
2504
787
0.078
81.8
3.57-3.75
3.2
0.085
8.5
1845
573
0.085
61.2
3.75-3.95
3.2
0.06
10.8
2062
638
0.06
73.8
3.95-4.19
3.2
0.049
11.9
2603
802
0.049
95.4
4.19-4.48
3.3
0.039
14
2331
711
0.039
90.8
4.48-4.84
3.3
0.036
15.7
1963
601
0.036
81.3
4.84-5.3
3.4
0.04
12.4
2221
660
0.04
96.5
5.3-5.93
3.3
0.04
15.3
1888
579
0.04
94.4
5.93-6.84
3.2
0.037
16.1
1534
478
0.037
85.7
6.84-8.38
3.2
0.033
16.1
1361
432
0.033
90.6
8.38-11.85
3.1
0.032
17.8
1091
357
0.032
94.6
11.85-44.544
2.8
0.042
10.5
570
200
0.042
86.4
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.1
dataextraction
SHELX
phasing
SHARP
phasing
SCALA
3.3.20
datascaling
REFMAC
5.7.0032
refinement
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.65→44.544 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 27.395 / SU ML: 0.262 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.589 / ESU R Free: 0.32 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. CHLORIDE (CL),SULFATE (SO4) AND GLYCEROL (GOL) MOLECULES FROM THE PURIFICATION/CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. 7. DUE TO STRONG ICE RINGS, REFLECTIONS WERE OMITTED IN THE 3.91-3.86 AND 3.70-3.64 RESOLUTION SHELLS LOWERING THE OVERALL COMPLETENESS TO 88.7%. THE NOMINAL RESOLUTION OF THE RESULTING DATASET IS 2.80 A WITH 2358 OBSERVED REFLECTIONS BETWEEN 2.80-2.65 (92.4% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2609
768
5.1 %
RANDOM
Rwork
0.2336
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obs
0.2351
15135
88.7 %
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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
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