- PDB-3dcz: CRYSTAL STRUCTURE OF A PUTATIVE RNFG SUBUNIT OF ELECTRON TRANSPOR... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 3dcz
Title
CRYSTAL STRUCTURE OF A PUTATIVE RNFG SUBUNIT OF ELECTRON TRANSPORT COMPLEX (TM0246) FROM THERMOTOGA MARITIMA AT 1.65 A RESOLUTION
Components
putative RnfG subunit of electron transport complex
Keywords
OXIDOREDUCTASE / PUTATIVE RNFG SUBUNIT OF ELECTRON TRANSPORT COMPLEX / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information
Translocases / FMN binding / electron transfer activity / membrane => GO:0016020 / plasma membrane Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE. ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 30-224 OF THE FULL LENGTH PROTEIN.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.27 Å3/Da / Density % sol: 45.73 %
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 14, 2008 / Details: Flat mirror (vertical focusing)
Radiation
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
0.91162
1
2
0.97932
1
3
0.97891
1
Reflection
Resolution: 1.65→29.148 Å / Num. obs: 25591 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.735 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 7.5
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
1.65-1.69
3.7
0.497
1.5
6885
1876
0.497
100
1.69-1.74
3.7
0.404
1.9
6662
1808
0.404
100
1.74-1.79
3.7
0.319
2.4
6524
1772
0.319
100
1.79-1.84
3.7
0.266
2.9
6336
1717
0.266
100
1.84-1.91
3.7
0.217
3.5
6206
1680
0.217
100
1.91-1.97
3.7
0.163
4.4
5907
1612
0.163
100
1.97-2.05
3.7
0.133
5.6
5804
1558
0.133
100
2.05-2.13
3.7
0.11
6.7
5499
1491
0.11
100
2.13-2.22
3.7
0.093
7.6
5399
1464
0.093
100
2.22-2.33
3.7
0.093
7.5
5146
1390
0.093
100
2.33-2.46
3.7
0.092
6.9
4829
1319
0.092
100
2.46-2.61
3.6
0.086
7.5
4520
1240
0.086
100
2.61-2.79
3.6
0.076
8.8
4306
1184
0.076
100
2.79-3.01
3.7
0.062
10.2
4054
1108
0.062
100
3.01-3.3
3.7
0.051
11.6
3760
1027
0.051
100
3.3-3.69
3.6
0.043
14.2
3338
922
0.043
100
3.69-4.26
3.6
0.041
14.5
2989
828
0.041
100
4.26-5.22
3.6
0.037
16
2520
705
0.037
100
5.22-7.38
3.5
0.041
15.2
1994
569
0.041
100
7.38-29.15
3.3
0.041
14.5
1045
321
0.041
97.5
-
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: 1.65→29.148 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.023 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.086 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. SO4,ACT,EDO MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.205
1304
5.1 %
RANDOM
Rwork
0.176
-
-
-
obs
0.177
25581
99.94 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 16.063 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.07 Å2
0 Å2
0 Å2
2-
-
-0.35 Å2
0 Å2
3-
-
-
0.28 Å2
Refinement step
Cycle: LAST / Resolution: 1.65→29.148 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1294
0
18
145
1457
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
1404
X-RAY DIFFRACTION
r_bond_other_d
0.005
0.02
959
X-RAY DIFFRACTION
r_angle_refined_deg
1.481
2.01
1915
X-RAY DIFFRACTION
r_angle_other_deg
0.898
3
2364
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.308
5
190
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.765
24.107
56
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.606
15
247
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.145
15
9
X-RAY DIFFRACTION
r_chiral_restr
0.092
0.2
224
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1552
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
273
X-RAY DIFFRACTION
r_nbd_refined
0.216
0.2
268
X-RAY DIFFRACTION
r_nbd_other
0.199
0.2
969
X-RAY DIFFRACTION
r_nbtor_refined
0.184
0.2
673
X-RAY DIFFRACTION
r_nbtor_other
0.087
0.2
744
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.156
0.2
128
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.261
0.2
21
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.314
0.2
25
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.163
0.2
18
X-RAY DIFFRACTION
r_mcbond_it
2.053
3
906
X-RAY DIFFRACTION
r_mcbond_other
0.489
3
356
X-RAY DIFFRACTION
r_mcangle_it
2.989
5
1433
X-RAY DIFFRACTION
r_scbond_it
4.256
8
553
X-RAY DIFFRACTION
r_scangle_it
6.114
11
470
LS refinement shell
Resolution: 1.65→1.693 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.263
105
-
Rwork
0.223
1771
-
all
-
1876
-
obs
-
-
100 %
Refinement TLS params.
Method: refined / Origin x: 31.2107 Å / Origin y: 35.4521 Å / Origin z: 18.5391 Å
11
12
13
21
22
23
31
32
33
T
-0.0385 Å2
-0.0145 Å2
-0.0078 Å2
-
-0.0296 Å2
-0.0066 Å2
-
-
-0.0461 Å2
L
1.2594 °2
0.0061 °2
-0.528 °2
-
1.3301 °2
0.2736 °2
-
-
1.0959 °2
S
0.0064 Å °
-0.0414 Å °
0.0615 Å °
0.0989 Å °
-0.0045 Å °
-0.0051 Å °
0.0431 Å °
-0.0387 Å °
-0.0019 Å °
+
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