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- PDB-6dm8: Understanding the Species Selectivity of Myeloid cell leukemia-1 ... -

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Basic information

Entry
Database: PDB / ID: 6dm8
TitleUnderstanding the Species Selectivity of Myeloid cell leukemia-1 (Mcl-1) inhibitors
ComponentsInduced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera
KeywordsSIGNALING PROTEIN/INHIBITOR / Apoptosis / cancer / Mcl-1 / drug discovery / SIGNALING PROTEIN / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


BH domain binding / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / channel activity / mitochondrial fusion / Bcl-2 family protein complex / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport ...BH domain binding / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / channel activity / mitochondrial fusion / Bcl-2 family protein complex / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / BH3 domain binding / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of anoikis / carbohydrate transport / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / negative regulation of autophagy / release of cytochrome c from mitochondria / response to cytokine / intrinsic apoptotic signaling pathway in response to DNA damage / outer membrane-bounded periplasmic space / regulation of apoptotic process / mitochondrial outer membrane / cell differentiation / periplasmic space / protein dimerization activity / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Apoptosis regulator, Mcl-1 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 ...Apoptosis regulator, Mcl-1 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / Chem-6AK / Maltose/maltodextrin-binding periplasmic protein / Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsZhao, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)BOA 29XS129TO22 United States
CitationJournal: Biochemistry / Year: 2018
Title: Understanding the Species Selectivity of Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors.
Authors: Zhao, B. / Arnold, A.L. / Coronel, M.A. / Lee, J.H. / Lee, T. / Olejniczak, E.T. / Fesik, S.W.
History
DepositionJun 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera
B: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera
C: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera
D: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera
E: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera
F: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera
G: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera
H: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)479,37140
Polymers459,5288
Non-polymers19,84232
Water8,521473
1
A: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9215
Polymers57,4411
Non-polymers2,4804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2094
Polymers57,4411
Non-polymers1,7683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6346
Polymers57,4411
Non-polymers3,1935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2094
Polymers57,4411
Non-polymers1,7683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2094
Polymers57,4411
Non-polymers1,7683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6346
Polymers57,4411
Non-polymers3,1935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9215
Polymers57,4411
Non-polymers2,4804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6346
Polymers57,4411
Non-polymers3,1935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.206, 104.153, 146.206
Angle α, β, γ (deg.)89.86, 89.80, 89.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Induced myeloid leukemia cell differentiation protein Mcl-1 homolog - MBP chimera / MBP / MMBP / Maltodextrin-binding protein / Bcl-2-related protein EAT/mcl1


Mass: 57441.062 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Mus musculus (house mouse)
Strain: K12 / Gene: malE, b4034, JW3994, Mcl1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: P97287
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical...
ChemComp-6AK / 4-{8-chloro-11-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-1-oxo-7-(1,3,5-trimethyl-1H-pyrazol-4-yl)-4,5-dihydro-1H-[1,4]diazepino[1,2-a]indol-2(3H)-yl}-1-methyl-1H-indole-6-carboxylic acid


Mass: 712.664 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C39H39Cl2N5O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG6000, Bicine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 123206 / % possible obs: 93.7 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.072 / Rrim(I) all: 0.115 / Rsym value: 0.089 / Χ2: 0.87 / Net I/σ(I): 8.83
Reflection shellResolution: 2.7→2.773 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.371 / Num. unique obs: 9265 / Rpim(I) all: 0.314 / Rrim(I) all: 0.488 / Rsym value: 0.657 / % possible all: 86.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.7→29.966 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2881 1765 1.43 %
Rwork0.2451 --
obs0.2458 123206 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→29.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30717 0 1384 473 32574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00333063
X-RAY DIFFRACTIONf_angle_d0.72145200
X-RAY DIFFRACTIONf_dihedral_angle_d7.69923764
X-RAY DIFFRACTIONf_chiral_restr0.0624858
X-RAY DIFFRACTIONf_plane_restr0.0045720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.7730.39761340.30999265X-RAY DIFFRACTION100
2.773-2.85450.39181410.3039362X-RAY DIFFRACTION100
2.8545-2.94650.33271330.29769362X-RAY DIFFRACTION100
2.9465-3.05180.33071400.2869383X-RAY DIFFRACTION100
3.0518-3.17380.31911340.28279295X-RAY DIFFRACTION100
3.1738-3.31810.34431370.27479379X-RAY DIFFRACTION100
3.3181-3.49280.33281390.2659325X-RAY DIFFRACTION100
3.4928-3.71120.30661320.25049298X-RAY DIFFRACTION100
3.7112-3.99720.2761220.23799398X-RAY DIFFRACTION100
3.9972-4.39830.24881320.22189318X-RAY DIFFRACTION100
4.3983-5.03220.24021420.20799391X-RAY DIFFRACTION100
5.0322-6.33010.29651350.23189359X-RAY DIFFRACTION100
6.3301-29.9680.21551440.20729306X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.7164-0.63590.02823.24110.64740.79620.1599-0.1776-0.0024-0.1464-0.0616-0.0529-0.001-0.0538-0.10250.2541-0.0555-0.01990.27340.0070.1205-161.1949-1.981746.2384
22.03030.1687-0.06211.938-0.99362.2552-0.0729-0.1515-0.1405-0.0395-0.01590.3174-0.0473-0.27120.00240.22630.0667-0.04440.2567-0.03820.3697-197.663-2.476136.8129
30.9255-0.56060.20683.4185-0.16081.1412-0.0348-0.1856-0.12410.09290.10310.39620.0394-0.1582-0.06070.1913-0.0070.03350.2810.08880.2143-152.7259-21.2748-26.0974
43.26650.387-0.91711.44840.34960.1541-0.104-0.3097-0.26550.12820.0418-0.40060.14630.0833-0.06970.37280.0287-0.09180.24410.04590.2699-124.8045-32.2797-31.8894
52.46330.1587-0.26782.29320.62281.92050.3034-0.10790.3726-0.0018-0.0491-0.5056-0.16860.0412-0.17230.34910.0567-0.01930.24770.03830.3894-116.2347-22.4334-39.277
62.36660.73850.51712.14740.57081.55310.01840.0120.25720.03460.0902-0.206-0.06270.1303-0.01980.2150.04080.05910.2417-0.01910.2087-160.459439.171410.1554
70.89730.37340.07872.72080.08620.81610.06180.1528-0.1716-0.1040.0123-0.38090.08990.1196-0.06990.23010.02290.00440.3257-0.05850.2056-157.975623.982610.0126
82.3155-0.72120.63382.1081-0.24891.54450.14470.24060.3479-0.0085-0.03160.3311-0.0723-0.0574-0.07630.2566-0.0604-0.02970.323-0.00250.4871-195.118727.695220.1219
92.7325-0.32240.18471.4445-0.16992.0942-0.2948-0.5621-0.19710.38560.06180.0723-0.0359-0.03660.12330.27050.14490.04160.3395-0.01410.2728-194.133350.408451.2054
104.1041-1.22210.37151.65970.03190.6069-0.10430.05110.149-0.33140.0441-0.08660.0371-0.030.00560.31680.0079-0.03420.40590.0140.2119-158.30151.048744.5976
111.37880.6063-0.15572.6905-0.25231.04890.06290.0973-0.00160.19890.04510.1284-0.05340.015-0.09770.24070.1027-0.03420.32540.04550.1588-148.480250.247683.2741
122.3823-0.8862-0.00151.30940.66162.01840.0140.36140.0167-0.0052-0.1165-0.20670.01170.05660.090.2993-0.0252-0.04120.2490.05870.3931-112.241749.807192.834
130.5483-0.1466-1.08031.17780.04992.1677-0.0490.6215-0.2838-0.58890.3859-0.1897-0.212-0.2250.11120.4791-0.2424-0.03630.6198-0.17530.4486-120.3258-10.070865.0355
143.17370.06420.20411.6187-0.38332.0298-0.17960.5222-0.1064-0.3642-0.084-0.1363-0.0530.10470.11390.2092-0.12480.03860.26490.03960.2664-114.23350.382281.4935
152.46790.6415-0.38181.6741-0.73940.30870.2118-0.8075-0.23660.4874-0.3447-0.0413-0.0043-0.21880.10260.5104-0.00470.01310.4398-0.0230.3951-151.2988-1.031887.8485
164.00030.7849-0.26963.1231-1.40612.72980.0059-0.0545-0.11420.1332-0.0115-0.02460.08370.2102-0.03050.19780.0664-0.08860.2642-0.04310.2196-151.2651-0.557382.0953
172.18450.46630.54162.0480.00642.1292-0.03190.10980.1965-0.35180.03190.234-0.1821-0.09720.04210.2614-0.0054-0.03740.19070.03710.2295-196.6835-23.71714.7917
181.90390.2155-0.35680.5871-0.22011.0168-0.0958-0.1030.25410.24340.0816-0.10820.15150.393-0.05160.3061-0.0187-0.01690.4193-0.04740.3238-175.2447-27.335815.5094
193.23250.79940.04283.19560.8542.5713-0.0380.07840.20660.2381-0.026-0.68210.05980.46760.17130.24880.00010.01140.46940.07120.342-157.8681-23.32688.6185
201.9969-0.16550.63511.8017-0.00351.6985-0.1214-0.16250.13550.40960.0406-0.1653-0.06010.04450.05940.28040.0321-0.04310.177-0.020.1951-115.1527.1418-22.5482
211.89570.00660.43430.97240.01661.1444-0.04140.60380.3842-1.5693-0.10930.42940.0388-0.4658-0.10010.76990.16920.01610.63580.21230.5667-150.412429.9691-36.6611
222.6609-0.4684-0.04592.5522-1.27972.4673-0.1178-0.01990.16290.00960.08960.229-0.1501-0.1867-0.07060.27440.01060.00280.4241-0.03970.2295-151.809128.7111-25.3981
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -215 through 154 )
2X-RAY DIFFRACTION2chain 'A' and (resid 155 through 301 )
3X-RAY DIFFRACTION3chain 'B' and (resid -214 through 118 )
4X-RAY DIFFRACTION4chain 'B' and (resid 119 through 204 )
5X-RAY DIFFRACTION5chain 'B' and (resid 205 through 301 )
6X-RAY DIFFRACTION6chain 'C' and (resid -214 through -83 )
7X-RAY DIFFRACTION7chain 'C' and (resid -82 through 154 )
8X-RAY DIFFRACTION8chain 'C' and (resid 155 through 302 )
9X-RAY DIFFRACTION9chain 'D' and (resid -214 through 141 )
10X-RAY DIFFRACTION10chain 'D' and (resid 142 through 301 )
11X-RAY DIFFRACTION11chain 'E' and (resid -215 through 154 )
12X-RAY DIFFRACTION12chain 'E' and (resid 155 through 301 )
13X-RAY DIFFRACTION13chain 'F' and (resid -214 through -143 )
14X-RAY DIFFRACTION14chain 'F' and (resid -142 through 141 )
15X-RAY DIFFRACTION15chain 'F' and (resid 142 through 220 )
16X-RAY DIFFRACTION16chain 'F' and (resid 221 through 301 )
17X-RAY DIFFRACTION17chain 'G' and (resid -214 through 99 )
18X-RAY DIFFRACTION18chain 'G' and (resid 100 through 200 )
19X-RAY DIFFRACTION19chain 'G' and (resid 201 through 301 )
20X-RAY DIFFRACTION20chain 'H' and (resid -214 through 154 )
21X-RAY DIFFRACTION21chain 'H' and (resid 155 through 204 )
22X-RAY DIFFRACTION22chain 'H' and (resid 205 through 297 )

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • 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

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