- PDB-3zdq: STRUCTURE OF THE HUMAN MITOCHONDRIAL ABC TRANSPORTER, ABCB10 (NUC... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 3zdq
Title
STRUCTURE OF THE HUMAN MITOCHONDRIAL ABC TRANSPORTER, ABCB10 (NUCLEOTIDE-FREE FORM)
Components
ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10, MITOCHONDRIAL
Keywords
HYDROLASE / MEMBRANE PROTEIN / MITOCHONDRIAL TRANSPORT
Function / homology
Function and homology information
export from the mitochondrion / positive regulation of heme biosynthetic process / Mitochondrial ABC transporters / mitochondrial unfolded protein response / positive regulation of hemoglobin biosynthetic process / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / heme biosynthetic process / mitochondrial transport / ABC-type transporter activity / erythrocyte development ...export from the mitochondrion / positive regulation of heme biosynthetic process / Mitochondrial ABC transporters / mitochondrial unfolded protein response / positive regulation of hemoglobin biosynthetic process / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / heme biosynthetic process / mitochondrial transport / ABC-type transporter activity / erythrocyte development / positive regulation of erythrocyte differentiation / mitochondrial membrane / mitochondrial inner membrane / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion binding Similarity search - Function
ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Resolution: 2.85→30.52 Å / Cor.coef. Fo:Fc: 0.9144 / Cor.coef. Fo:Fc free: 0.8869 / SU R Cruickshank DPI: 0.645 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.584 / SU Rfree Blow DPI: 0.307 / SU Rfree Cruickshank DPI: 0.318 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2444
1101
5.15 %
RANDOM
Rwork
0.2021
-
-
-
obs
0.2042
21397
99.97 %
-
Displacement parameters
Biso mean: 75 Å2
Baniso -1
Baniso -2
Baniso -3
1-
7.47 Å2
0 Å2
0 Å2
2-
-
7.47 Å2
0 Å2
3-
-
-
-14.94 Å2
Refine analyze
Luzzati coordinate error obs: 0.393 Å
Refinement step
Cycle: LAST / Resolution: 2.85→30.52 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4239
0
186
30
4455
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
4506
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.06
6084
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
2145
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
81
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
659
HARMONIC
5
X-RAY DIFFRACTION
t_it
4506
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.47
X-RAY DIFFRACTION
t_other_torsion
3.23
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
608
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
5197
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.85→2.99 Å / Total num. of bins used: 11
Rfactor
Num. reflection
% reflection
Rfree
0.244
157
5.56 %
Rwork
0.2178
2667
-
all
0.2194
2824
-
obs
-
-
99.97 %
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
0.9666
-0.908
0.1011
3.4144
0.6137
0.1892
0.1483
0.1089
0.0158
-0.169
0.112
0.1933
0.1074
-0.1986
-0.2603
-0.0372
0.075
0.096
-0.1679
0.0689
0.0779
-64.0668
76.8657
7.9985
2
-0.336
0.4394
-0.0117
1.3898
-0.8709
0
0.1591
0.1099
-0.0674
-0.171
0.0028
0.2783
0.0405
-0.1442
-0.1618
0.1056
0.0953
-0.0057
-0.1843
0.0529
0.0356
-48.7883
60.1393
-0.5699
3
1.8459
-2.8727
1.321
4.4136
-1.1782
0.676
0.2619
0.1573
0.043
-0.407
-0.1715
-0.1186
-0.2505
-0.1105
-0.0904
-0.0774
0.2068
0.0246
-0.0401
0.02
-0.037
-15.3942
62.2897
0.3814
4
0.5167
-0.3719
-0.0337
3.1973
-0.6338
0
0.0317
0.0814
-0.0117
0.0395
-0.0014
0.0385
-0.0716
-0.052
-0.0303
0.0175
0.1076
-0.0087
-0.1301
-0.0001
-0.1516
-42.1794
50.4873
-3.0227
5
2.2343
-0.4636
-0.4587
2.9557
1.0898
6.395
-0.0257
-0.3165
-0.264
0.3395
0.1136
-0.2245
-0.0132
0.6313
-0.0878
-0.2506
-0.0002
-0.0821
-0.2582
0.0717
-0.0204
-31.5712
16.662
13.415
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAIN A AND RESSEQ 153 - 232
2
X-RAY DIFFRACTION
2
CHAIN A AND RESSEQ 233 - 331
3
X-RAY DIFFRACTION
3
CHAIN A AND RESSEQ 332 - 397
4
X-RAY DIFFRACTION
4
CHAIN A AND RESSEQ 398 - 528
5
X-RAY DIFFRACTION
5
CHAIN A AND RESSEQ 529 - 722
+
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