- PDB-4djn: Crystal structure of a ribonucleotide reductase M2 B (RNRR2) from... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4djn
Title
Crystal structure of a ribonucleotide reductase M2 B (RNRR2) from Homo sapiens at 2.20 A resolution
Components
Ribonucleoside-diphosphate reductase subunit M2 B
Keywords
OXIDOREDUCTASE / DNA REPLICATION / P53 INDUCIBLE / METAL-BINDING / NUCLEUS / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information
deoxyribonucleoside triphosphate metabolic process / ribonucleoside diphosphate metabolic process / positive regulation of G0 to G1 transition / 2'-deoxyribonucleotide biosynthetic process / mitochondrial DNA replication / renal system process / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor ...deoxyribonucleoside triphosphate metabolic process / ribonucleoside diphosphate metabolic process / positive regulation of G0 to G1 transition / 2'-deoxyribonucleotide biosynthetic process / mitochondrial DNA replication / renal system process / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / Interconversion of nucleotide di- and triphosphates / deoxyribonucleotide biosynthetic process / DNA synthesis involved in DNA repair / response to amine / positive regulation of G2/M transition of mitotic cell cycle / kidney development / TP53 Regulates Metabolic Genes / response to oxidative stress / DNA repair / mitochondrion / nucleoplasm / identical protein binding / metal ion binding / cytosol Similarity search - Function
Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 121 / 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 13-322 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: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2.0M ammonium sulfate, 0.1M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97895 Å / Relative weight: 1
Reflection
Resolution: 2.2→29.834 Å / Num. all: 45830 / Num. obs: 45830 / % possible obs: 97.5 % / Redundancy: 6.3 % / Rsym value: 0.105 / Net I/σ(I): 9.8
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
2.2-2.26
3.9
0.73
1.7
12292
3169
0.73
95.8
2.26-2.32
3.8
0.634
1.9
12525
3325
0.634
98.7
2.32-2.39
3.7
0.513
2.3
11754
3203
0.513
98.5
2.39-2.46
3.6
0.387
2.9
11135
3124
0.387
97.6
2.46-2.54
3.4
0.311
3.4
9692
2853
0.311
93.5
2.54-2.63
7.9
0.533
4.6
23452
2950
0.533
99.2
2.63-2.73
7.9
0.416
5.5
22661
2860
0.416
98.9
2.73-2.84
7.8
0.321
6.5
21538
2751
0.321
99.2
2.84-2.97
7.7
0.236
8
20306
2630
0.236
98.9
2.97-3.11
7.6
0.179
9.7
19341
2530
0.179
98.6
3.11-3.28
6.7
0.141
10.7
15482
2300
0.141
94.2
3.28-3.48
8
0.11
14.4
18072
2261
0.11
98.8
3.48-3.72
8.1
0.09
17.2
17491
2168
0.09
99.3
3.72-4.02
7.8
0.081
19.9
15796
2032
0.081
99.4
4.02-4.4
7.6
0.076
22.2
14073
1842
0.076
98.5
4.4-4.92
6.6
0.072
22.6
10416
1569
0.072
92.9
4.92-5.68
8
0.078
23.3
11920
1484
0.078
97.9
5.68-6.96
7.9
0.089
21.7
9985
1262
0.089
96.8
6.96-9.84
6.8
0.062
26.5
6433
949
0.062
92.4
9.84-29.834
7.9
0.053
32.8
4513
568
0.053
94.2
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Phasing
Phasing
Method: SAD
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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
5.6.0117
refinement
MOSFLM
datareduction
SHELXD
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.2→29.834 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 10.232 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.165 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS 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. SULFATE ION (SO4) AND 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. 7. NCS RESTRAINTS WERE APPLIED USING REFMAC's LOCAL NCS OPTION (NCSR LOCAL). NCS GROUP 1 CHAIN A (28-312) TO CHAIN B (28-312) COUNT: 9996, RMS: 0.16, WEIGHT: 0.05.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2191
2320
5.1 %
RANDOM
Rwork
0.1931
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obs
0.1945
45754
97.14 %
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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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