- PDB-3dkq: Crystal structure of Putative Oxygenase (YP_001051978.1) from SHE... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 3dkq
Title
Crystal structure of Putative Oxygenase (YP_001051978.1) from SHEWANELLA BALTICA OS155 at 2.26 A resolution
Components
PKHD-type hydroxylase Sbal_3634
Keywords
OXIDOREDUCTASE / YP_001051978.1 / Putative Oxygenase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Dioxygenase / Iron / Metal-binding / Vitamin C
Function / homology
Function and homology information
Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / 2-oxoglutarate-dependent dioxygenase activity / L-ascorbic acid binding / iron ion binding Similarity search - Function
AUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A NONAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. HOWEVER, THIS STATE IS NOT REPRESENTED IN THE CRYSTAL LATTICE.
Mass: 27978.312 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella baltica OS155 (bacteria) / Gene: YP_001051978.1, Sbal_3634 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 References: UniProt: A3D8P6, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
Resolution: 2.26→28.855 Å / Num. obs: 47944 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 39.52 Å2 / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 5.8
Reflection shell
Resolution: 2.26→2.32 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 0.9 / Rsym value: 0.871 / % possible all: 100
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
3.004
dataextraction
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.26→28.855 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.871 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.188 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORAT 4. X-RAY FLUORESCENCE EXCITATION AND WAVELENGTH SCANS AND ANOMALOUS DIFFERENCE FOURIERS SUPPORT THE MODELING OF NI IONS. 5. GOL AND IMD MOLECULES FROM THE CRYO/ CRYSTALLIZATION SOLUTIONS 6. IMIDAZOLE HAS BEEN TENTATIVELY MODELED NEXT TO NI SITES ON THE BASIS OF THE DENSITY AND CRYSTALLIZATION CONDITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.232
2424
5.1 %
RANDOM
Rwork
0.196
-
-
-
obs
0.198
47880
99.9 %
-
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: 45.33 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.11 Å2
0 Å2
0 Å2
2-
-
1.11 Å2
0 Å2
3-
-
-
-2.23 Å2
Refinement step
Cycle: LAST / Resolution: 2.26→28.855 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5198
0
69
244
5511
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
5463
X-RAY DIFFRACTION
r_bond_other_d
0.004
0.02
3725
X-RAY DIFFRACTION
r_angle_refined_deg
1.643
1.965
7404
X-RAY DIFFRACTION
r_angle_other_deg
1.339
3
9047
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.945
5
678
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.04
24.373
279
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.809
15
917
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.722
15
42
X-RAY DIFFRACTION
r_chiral_restr
0.094
0.2
809
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
6141
X-RAY DIFFRACTION
r_gen_planes_other
0.003
0.02
1136
X-RAY DIFFRACTION
r_nbd_refined
0.181
0.2
991
X-RAY DIFFRACTION
r_nbd_other
0.149
0.2
3709
X-RAY DIFFRACTION
r_nbtor_refined
0.154
0.2
2525
X-RAY DIFFRACTION
r_nbtor_other
0.073
0.2
2884
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.103
0.2
247
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.129
0.2
14
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.278
0.2
52
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.118
0.2
16
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.295
2
3792
X-RAY DIFFRACTION
r_mcbond_other
0.317
2
1340
X-RAY DIFFRACTION
r_mcangle_it
2.054
4
5331
X-RAY DIFFRACTION
r_scbond_it
3.898
6
2339
X-RAY DIFFRACTION
r_scangle_it
5.227
8
2061
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
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
1164
MEDIUMPOSITIONAL
0.3
0.5
2
B
1164
MEDIUMPOSITIONAL
0.57
0.5
3
C
1164
MEDIUMPOSITIONAL
0.38
0.5
1
A
1358
LOOSEPOSITIONAL
0.51
5
2
B
1358
LOOSEPOSITIONAL
0.75
5
3
C
1358
LOOSEPOSITIONAL
0.58
5
1
A
1164
MEDIUMTHERMAL
0.94
2
2
B
1164
MEDIUMTHERMAL
1.1
2
3
C
1164
MEDIUMTHERMAL
1.03
2
1
A
1358
LOOSETHERMAL
2.12
10
2
B
1358
LOOSETHERMAL
2.85
10
3
C
1358
LOOSETHERMAL
2.45
10
LS refinement shell
Resolution: 2.26→2.32 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.287
164
-
Rwork
0.247
3316
-
obs
-
-
100 %
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
1.9767
-0.2442
0.8592
0.5148
0.1312
1.2901
-0.0071
-0.1653
0.0095
0.0257
-0.014
0.0392
-0.1615
-0.0727
0.0211
-0.1118
-0.0154
0.003
-0.1488
0.0199
-0.0666
74.603
109.665
-6.578
2
3.7746
-3.1282
0.6148
2.8715
-0.6862
0.6633
0.5349
0.5744
-0.4375
-0.4542
-0.5207
0.4159
0.0708
0.0492
-0.0142
0.0849
0.1423
-0.0489
0.0196
-0.0852
0.0145
41.168
125.689
-39.325
3
0.362
0.4081
-0.3275
2.052
-2.3192
4.2393
0.0951
0.1368
-0.0678
-0.0874
-0.3422
-0.3213
-0.1549
0.7684
0.2471
-0.0951
0.0181
0.052
0.0679
0.0355
-0.0036
72.087
102.983
-41.967
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
-5 - 224
14 - 243
2
X-RAY DIFFRACTION
2
B
B
-5 - 29
14 - 48
3
X-RAY DIFFRACTION
2
B
B
42 - 98
61 - 117
4
X-RAY DIFFRACTION
2
B
B
110 - 224
129 - 243
5
X-RAY DIFFRACTION
3
C
C
-4 - 31
15 - 50
6
X-RAY DIFFRACTION
3
C
C
40 - 224
59 - 243
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi