- PDB-4q62: Crystal Structure of Leucine-rich repeat- and Coiled coil-contain... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 4q62
Title
Crystal Structure of Leucine-rich repeat- and Coiled coil-containing Protein from Legionella pneumophila
Components
Leucine-rich repeat-and coiled coil-containing protein
Keywords
UNKNOWN FUNCTION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Program for the Characterization of Secreted Effector Proteins / PCSEP / Leucine-rich repeats / coiled-coil
Resolution: 1.9→1.93 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 1377 / Rsym value: 0.465 / % possible all: 76.8
-
Processing
Software
Name
Version
Classification
SBC-Collect
datacollection
HKL-3000
datacollection
PHENIX
modelbuilding
HKL-3000
phasing
PHENIX
(phenix.refine: 1.8.1_1161)
refinement
HKL-3000
datareduction
HKL-3000
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.898→35.833 Å / SU ML: 0.18 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.59 / Stereochemistry target values: MLHL Details: number of total reflections include anomalous Friedel pairs
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.209
3245
5.04 %
random
Rwork
0.176
-
-
-
obs
0.177
64362
91.84 %
-
all
-
64362
-
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 26.6 Å2
Refinement step
Cycle: LAST / Resolution: 1.898→35.833 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3071
0
75
237
3383
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
3260
X-RAY DIFFRACTION
f_angle_d
1.009
4396
X-RAY DIFFRACTION
f_dihedral_angle_d
12.71
1247
X-RAY DIFFRACTION
f_chiral_restr
0.069
515
X-RAY DIFFRACTION
f_plane_restr
0.004
561
LS refinement shell
Refine-ID: X-RAY DIFFRACTION
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Num. reflection obs
% reflection obs (%)
1.8982-1.9265
0.3191
106
0.2764
1869
1975
64
1.9265-1.9566
0.3621
100
0.2656
2124
2224
74
1.9566-1.9887
0.2312
118
0.2366
2240
2358
76
1.9887-2.023
0.2753
112
0.2336
2235
2347
79
2.023-2.0598
0.2293
129
0.2216
2466
2595
83
2.0598-2.0994
0.2174
147
0.218
2439
2586
86
2.0994-2.1422
0.3176
144
0.1949
2606
2750
90
2.1422-2.1888
0.211
138
0.1926
2674
2812
92
2.1888-2.2397
0.2122
154
0.1856
2746
2900
95
2.2397-2.2957
0.1874
148
0.1838
2806
2954
97
2.2957-2.3578
0.2235
132
0.1838
2934
3066
99
2.3578-2.4271
0.2212
153
0.1813
2821
2974
99
2.4271-2.5054
0.2099
121
0.1734
2953
3074
99
2.5054-2.595
0.2044
167
0.167
2822
2989
99
2.595-2.6988
0.1821
148
0.1694
2856
3014
99
2.6988-2.8216
0.2083
135
0.1679
2905
3040
99
2.8216-2.9703
0.2098
175
0.1696
2854
3029
99
2.9703-3.1563
0.2055
175
0.1722
2871
3046
99
3.1563-3.3998
0.2158
168
0.1667
2801
2969
98
3.3998-3.7416
0.1834
137
0.1456
2797
2934
96
3.7416-4.2823
0.1868
153
0.143
2700
2853
95
4.2823-5.3923
0.1758
140
0.1623
2830
2970
97
5.3923-35.8397
0.2253
145
0.1946
2768
2913
96
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
0.7883
0.0188
-0.3534
2.6178
0.0463
0.9874
0.0315
0.1201
0.2407
-0.2623
0.0405
0.217
-0.0769
-0.1929
0.0068
0.0726
-0.0029
-0.0807
0.154
0.0311
0.1736
-21.0259
119.3925
7.4866
2
1.2891
-0.2375
0.2189
0.9647
0.0141
0.8561
-0.1142
0.1101
-0.1163
-0.1319
0.0258
-0.0449
0.1668
0.0505
0.0516
0.1495
-0.0091
0.0447
0.0691
-0.0092
0.0744
-5.2082
92.359
13.3128
3
2.762
-0.0588
-0.4074
2.899
-0.1407
3.2543
-0.0367
-0.2247
0.1257
-0.097
0.1963
-0.8382
-0.6782
0.8028
-0.0195
0.2493
-0.0856
0.0645
0.2604
-0.0678
0.3417
19.0982
104.0072
26.4643
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid3through152 )
2
X-RAY DIFFRACTION
2
chain 'A' and (resid153through312 )
3
X-RAY DIFFRACTION
3
chain 'A' and (resid313through415 )
+
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