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- PDB-5akb: MutS in complex with the N-terminal domain of MutL - crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 5akb
TitleMutS in complex with the N-terminal domain of MutL - crystal form 1
Components
  • DNA MISMATCH REPAIR PROTEIN MUTL
  • DNA MISMATCH REPAIR PROTEIN MUTS
KeywordsDNA BINDING PROTEIN / HYDROLASE / DNA MISMATCH REPAIR / COMPLEX / SLIDING CLAMP / CROSSLINKING
Function / homology
Function and homology information


single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / nucleotide-excision repair, DNA duplex unwinding / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity ...single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / nucleotide-excision repair, DNA duplex unwinding / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding / DNA damage response / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
DNA mismatch repair protein, MutL / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein MutS / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like ...DNA mismatch repair protein, MutL / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein MutS / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair proteins mutL / hexB / PMS1 signature. / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair protein MutS/MSH / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, clamp / DNA mismatch repair protein MutS, N-terminal / MutS, connector domain superfamily / MutS domain I / MutS domain II / MutS family domain IV / MutS domain III / DNA mismatch repair MutS family / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, core / DNA mismatch repair protein MutS, core domain superfamily / MutS domain V / DNA mismatch repair proteins mutS family signature. / DNA-binding domain of DNA mismatch repair MUTS family / ATPase domain of DNA mismatch repair MUTS family / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA mismatch repair protein MutL / DNA mismatch repair protein MutS
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.71 Å
AuthorsGroothuizen, F.S. / Winkler, I. / Cristovao, M. / Fish, A. / Winterwerp, H.H.K. / Reumer, A. / Marx, A.D. / Hermans, N. / Nicholls, R.A. / Murshudov, G.N. ...Groothuizen, F.S. / Winkler, I. / Cristovao, M. / Fish, A. / Winterwerp, H.H.K. / Reumer, A. / Marx, A.D. / Hermans, N. / Nicholls, R.A. / Murshudov, G.N. / Lebbink, J.H.G. / Friedhoff, P. / Sixma, T.K.
CitationJournal: Elife / Year: 2015
Title: MutS/MutL crystal structure reveals that the MutS sliding clamp loads MutL onto DNA.
Authors: Groothuizen, F.S. / Winkler, I. / Cristovao, M. / Fish, A. / Winterwerp, H.H. / Reumer, A. / Marx, A.D. / Hermans, N. / Nicholls, R.A. / Murshudov, G.N. / Lebbink, J.H. / Friedhoff, P. / Sixma, T.K.
History
DepositionMar 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Other
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_database_status
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_database_status.recvd_author_approval
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA MISMATCH REPAIR PROTEIN MUTS
B: DNA MISMATCH REPAIR PROTEIN MUTS
C: DNA MISMATCH REPAIR PROTEIN MUTL
D: DNA MISMATCH REPAIR PROTEIN MUTL
E: DNA MISMATCH REPAIR PROTEIN MUTS
F: DNA MISMATCH REPAIR PROTEIN MUTL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)393,7749
Polymers392,2556
Non-polymers1,5193
Water00
1
A: DNA MISMATCH REPAIR PROTEIN MUTS
B: DNA MISMATCH REPAIR PROTEIN MUTS
C: DNA MISMATCH REPAIR PROTEIN MUTL
D: DNA MISMATCH REPAIR PROTEIN MUTL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,5166
Polymers261,5044
Non-polymers1,0122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-4 kcal/mol
Surface area57860 Å2
MethodPQS
2
E: DNA MISMATCH REPAIR PROTEIN MUTS
F: DNA MISMATCH REPAIR PROTEIN MUTL
hetero molecules

E: DNA MISMATCH REPAIR PROTEIN MUTS
F: DNA MISMATCH REPAIR PROTEIN MUTL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,5166
Polymers261,5044
Non-polymers1,0122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_858-x+3,y,-z+31
Buried area1450 Å2
ΔGint-6.2 kcal/mol
Surface area52070 Å2
MethodPQS
Unit cell
Length a, b, c (Å)165.932, 188.544, 200.426
Angle α, β, γ (deg.)90.00, 94.77, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22E
13B
23E
14C
24D
15C
25F
16D
26F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGSERSERAA128 - 800128 - 800
21ARGARGSERSERBB128 - 800128 - 800
12ARGARGSERSERAA128 - 800128 - 800
22ARGARGSERSEREE128 - 800128 - 800
13ARGARGSERSERBB128 - 800128 - 800
23ARGARGSERSEREE128 - 800128 - 800
14VALVALGLNGLNCC20 - 33140 - 351
24VALVALGLNGLNDD20 - 33140 - 351
15VALVALGLNGLNCC20 - 33140 - 351
25VALVALGLNGLNFF20 - 33140 - 351
16VALVALGLNGLNDD20 - 33140 - 351
26VALVALGLNGLNFF20 - 33140 - 351

NCS ensembles :
ID
1
2
3
4
5
6
DetailsIN THIS STRUCTURE SINGLE CYSTEINES IN MUTS AND THE LN40 DOMAIN OF MUTL HAVE BEEN PLACED SUCH THAT CROSSLINKING OCCURS ONLY IN THE PRESENCE OF A DNA MISMATCH AND A NUCLEOTIDE (SEE WINKLER ET AL 2011, JBC). TO OBTAIN HOMOGENEOUS MATERIAL BOTH MUTS SUBUNITS HAVE BEEN CROSSLINKED TO A MUTL(LN40), WHEREAS FOR BIOLOGICAL FUNCTION ONLY ONE MUTL PER MUTS DIMER IS REQUIRED.

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Components

#1: Protein DNA MISMATCH REPAIR PROTEIN MUTS


Mass: 89476.086 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: BM(PEO)3 (THIOETHER) CROSSLINK BETWEEN-A 246 AND D 131, B 246 AND C 131, E 246 AND F 131
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) / Variant (production host): PLYSS / References: UniProt: P23909
#2: Protein DNA MISMATCH REPAIR PROTEIN MUTL


Mass: 41275.738 Da / Num. of mol.: 3 / Fragment: N-TERMINAL DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) / Variant (production host): PLYSS / References: UniProt: P23367
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
Sequence detailsNATIVE CYSTEINES REPLACED AND ONE CYSTEINE INTRODUCED N-TERMINAL HIS-TAG. NATIVE CYSTEINES REPLACED ...NATIVE CYSTEINES REPLACED AND ONE CYSTEINE INTRODUCED N-TERMINAL HIS-TAG. NATIVE CYSTEINES REPLACED AND ONE CYSTEINE INTRODUCED

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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: 3.98 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growDetails: 9-12% PEG8000, 100 MM TRIS PH 7.0, 200 MM MGCL2, 80-450 MM SODIUM MALONATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 4.71→82.7 Å / Num. obs: 31052 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 2.5
Reflection shellResolution: 4.71→4.96 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1W7A AND 1BKN

1w7a

1bkn


Resolution: 4.71→199.73 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.87 / SU B: 586.437 / SU ML: 2.651 / Cross valid method: THROUGHOUT / ESU R Free: 1.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED RESIDUES ABE1-127, ABE660-669, E442-516, CDF1-19, CDF74-79, CDF126-131, CDF300-314, CDF332-349 ARE DISORDERED. CROSSLINKER BMPEO3 IS DISORDERED. IN THIS STRUCTURE ...Details: U VALUES WITH TLS ADDED RESIDUES ABE1-127, ABE660-669, E442-516, CDF1-19, CDF74-79, CDF126-131, CDF300-314, CDF332-349 ARE DISORDERED. CROSSLINKER BMPEO3 IS DISORDERED. IN THIS STRUCTURE SINGLE CYSTEINES IN MUTS AND THE LN40 DOMAIN OF MUTL HAVE BEEN PLACED SUCH THAT CROSSLINKING OCCURS ONLY IN THE PRESENCE OF A DNA MISMATCH AND A NUCLEOTIDE (SEE WINKLER ET AL 2011, JBC). TO OBTAIN HOMOGENEOUS MATERIAL BOTH MUTS SUBUNIT HAVE BEEN CROSSLINKED TO A MUTL(LN40), WHEREAS FOR BIOLOGICAL FUNCTION ONLY ONE MUTL PER MUTS DIMER IS REQUIRED.
RfactorNum. reflection% reflectionSelection details
Rfree0.34918 1499 4.8 %RANDOM
Rwork0.31939 ---
obs0.32088 29545 97.23 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 234.958 Å2
Baniso -1Baniso -2Baniso -3
1--11.07 Å20 Å2-6.76 Å2
2---13.9 Å20 Å2
3---25.75 Å2
Refinement stepCycle: LAST / Resolution: 4.71→199.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21813 0 93 0 21906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01922263
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.97730153
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.37552750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29123.3081061
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.613153917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.77315235
X-RAY DIFFRACTIONr_chiral_restr0.0830.23448
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116760
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.276.48911055
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.6949.72413787
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4226.52511201
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined20.78460.14290637
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A17460.07
12B17460.07
21A12360.31
22E12360.31
31B12340.32
32E12340.32
41C7220.06
42D7220.06
51C7460.06
52F7460.06
61D7200.07
62F7200.07
LS refinement shellResolution: 4.71→4.832 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 111 -
Rwork0.45 2230 -
obs--97.83 %
Refinement TLS params.

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

IDL11 (°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)
13.96583.06771.18432.61991.05430.4349-0.3877-0.4913-0.05020.26870.16510.31760.16660.10720.22262.48970.71540.78463.22340.04310.8664192.0585-2.8862270.6282
22.348-1.76781.69453.9109-0.74072.251-0.1751-0.3041-0.36780.4340.21931.01050.2288-0.0016-0.04421.78470.14040.72683.10120.11270.4838203.0412-11.3925237.9357
30.0908-0.34960.14071.9959-0.69070.2525-0.09480.11070.1884-0.2106-0.031-0.0793-0.03680.08820.12582.1404-0.04170.09582.3667-0.02461.9478189.120341.2253196.9357
45.04551.5285-0.68630.5156-0.56984.7445-0.1711-0.0746-0.6281-0.0535-0.1728-0.3719-0.16050.17570.34381.87550.29530.2052.1216-0.17161.9901243.7167-13.9646252.5531
52.72822.57051.70512.51881.66161.1332-0.11540.0510.4233-0.02090.10890.1372-0.30070.03540.00652.2370.19880.47853.0195-0.390.9868243.65315.4063224.9999
62.0797-1.43241.22562.3482-1.0972.2555-0.554-0.66411.36810.32430.0387-0.6875-0.01470.07290.51532.16610.41520.15343.1968-0.93971.187222.373222.0586248.2453
71.41230.9445-0.50294.4987-1.03810.6164-0.21340.20450.04010.28630.44570.1530.0963-0.0223-0.23231.96280.05480.0112.126-0.01111.8291162.714834.6791220.3844
89.53932.23643.222812.9063-2.64812.02870.293-0.4444-0.276-0.2706-0.2122-0.11190.1037-0.1631-0.08082.12420.21190.2832.4485-0.30521.0923223.694-12.535274.2528
94.48092.92221.45942.58310.17011.7859-0.6747-0.0497-0.38730.28740.4618-0.3195-0.53530.06980.21292.20260.37720.63713.1429-0.30880.3852230.6202-23.4052218.0139
101.837-0.44770.12860.86650.76912.5814-0.0302-0.1711-0.0323-0.42860.07490.12220.0029-0.3818-0.04471.9216-0.0610.10942.14070.07331.6859208.4706-34.4481197.8721
111.74710.91640.65361.8019-0.48640.779-0.077-0.30010.44030.1235-0.03570.1589-0.1242-0.04040.11272.08350.12330.15442.2901-0.25221.8875209.443423.726280.7063
121.4575-0.0111-0.32631.9453-0.44260.187-0.0674-0.07570.0531-0.35980.17630.31-0.02040.0823-0.1092.15010.03550.072.2769-0.06411.9784206.377955.2018276.3421
131.6509-0.5307-1.07341.6692-0.82321.76790.0880.1022-0.03850.00550.2007-0.2190.0625-0.1132-0.28871.98650.020.01582.1792-0.00761.8034243.935-54.9532269.9471
140.07060.0904-0.09911.4495-0.15090.16920.03260.0508-0.0568-0.09670.0427-0.07970.109-0.0279-0.07531.9369-0.03140.12782.23290.02571.7701212.7917-65.1789283.3903
153.4605-3.6269-0.62763.90750.68350.1358-0.3274-0.2411-0.2895-0.0250.36230.5902-0.15960.0362-0.03492.2737-0.06450.24352.36970.18432.1772212.587-27.051305.8473
160.2171-0.01170.60881.37370.45271.91250.04630.0251-0.0477-0.05980.09990.1348-0.1022-0.029-0.14621.8495-0.0480.10872.2840.12141.981183.9557-54.7212301.7071
170.1083-0.0493-0.27281.01831.0741.77220.06810.1678-0.15190.2864-0.12250.06850.3335-0.08130.05442.0593-0.0473-0.01122.27470.00542.1507168.9275-78.0271285.8062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A128 - 266
2X-RAY DIFFRACTION2A267 - 442
3X-RAY DIFFRACTION2A517 - 765
4X-RAY DIFFRACTION2A1800 - 1802
5X-RAY DIFFRACTION3A443 - 516
6X-RAY DIFFRACTION4A766 - 800
7X-RAY DIFFRACTION5B128 - 266
8X-RAY DIFFRACTION6B267 - 442
9X-RAY DIFFRACTION6B517 - 765
10X-RAY DIFFRACTION6B1800 - 1802
11X-RAY DIFFRACTION7B443 - 516
12X-RAY DIFFRACTION8B766 - 800
13X-RAY DIFFRACTION9C20 - 204
14X-RAY DIFFRACTION10C205 - 331
15X-RAY DIFFRACTION11D20 - 204
16X-RAY DIFFRACTION12D205 - 331
17X-RAY DIFFRACTION13E128 - 266
18X-RAY DIFFRACTION14E267 - 765
19X-RAY DIFFRACTION14E1800 - 1802
20X-RAY DIFFRACTION15E766 - 800
21X-RAY DIFFRACTION16F20 - 204
22X-RAY DIFFRACTION17F205 - 331

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  • 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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