[English] 日本語
Yorodumi
- PDB-7jj8: Crystal structure of the Zn(II)-bound ZnuA-like domain of Strepto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jj8
TitleCrystal structure of the Zn(II)-bound ZnuA-like domain of Streptococcus pneumoniae AdcA
ComponentsZinc-binding lipoprotein AdcA
KeywordsMETAL BINDING PROTEIN / AdcA / ZnuA / SBP / ATP-binding cassette transporter / Zn acquisition
Function / homology
Function and homology information


zinc ion transport / establishment of competence for transformation / cell adhesion / zinc ion binding / plasma membrane
Similarity search - Function
ZinT domain / ZinT (YodA) periplasmic lipocalin-like zinc-recruitment / Adhesin B / Adhesion lipoprotein / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Calycin / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Zinc-binding lipoprotein AdcA
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsLuo, Z. / More, J.R. / Kobe, B. / McDevitt, C.A.
Funding support Australia, 4items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1071659 Australia
National Health and Medical Research Council (NHMRC, Australia)1080784 Australia
National Health and Medical Research Council (NHMRC, Australia)1122582 Australia
Australian Research Council (ARC)DP170102102 Australia
CitationJournal: Mbio / Year: 2021
Title: A Trap-Door Mechanism for Zinc Acquisition by Streptococcus pneumoniae AdcA.
Authors: Luo, Z. / Morey, J.R. / Deplazes, E. / Motygullina, A. / Tan, A. / Ganio, K. / Neville, S.L. / Eleftheriadis, N. / Isselstein, M. / Pederick, V.G. / Paton, J.C. / Cordes, T. / Harmer, J.R. / ...Authors: Luo, Z. / Morey, J.R. / Deplazes, E. / Motygullina, A. / Tan, A. / Ganio, K. / Neville, S.L. / Eleftheriadis, N. / Isselstein, M. / Pederick, V.G. / Paton, J.C. / Cordes, T. / Harmer, J.R. / Kobe, B. / McDevitt, C.A.
History
DepositionJul 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Zinc-binding lipoprotein AdcA
A: Zinc-binding lipoprotein AdcA
C: Zinc-binding lipoprotein AdcA
D: Zinc-binding lipoprotein AdcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,0748
Polymers132,8124
Non-polymers2624
Water8,323462
1
B: Zinc-binding lipoprotein AdcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2682
Polymers33,2031
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Zinc-binding lipoprotein AdcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2682
Polymers33,2031
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Zinc-binding lipoprotein AdcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2682
Polymers33,2031
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Zinc-binding lipoprotein AdcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2682
Polymers33,2031
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.372, 67.956, 79.622
Angle α, β, γ (deg.)92.275, 104.697, 115.959
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYSERSER(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB27 - 681 - 42
12ALAALAGLNGLN(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB71 - 7645 - 50
13ALAALAPROPRO(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB78 - 9352 - 67
14LEULEULEULEU(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB95 - 9969 - 73
15LYSLYSGLYGLY(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB102 - 11876 - 92
16PHEPHELYSLYS(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB137 - 167111 - 141
17THRTHRGLNGLN(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB169 - 194143 - 168
18GLNGLNASPASP(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB197 - 227171 - 201
19PROPROLYSLYS(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB230 - 243204 - 217
110ASNASNSERSER(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB245 - 265219 - 239
111GLUGLUTHRTHR(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB267 - 282241 - 256
112ASPASPTHRTHR(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB285 - 286259 - 260
113ALAALAASPASP(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB288 - 308262 - 282
21GLYGLYSERSER(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA27 - 681 - 42
22ALAALAGLNGLN(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA71 - 7645 - 50
23ALAALAPROPRO(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA78 - 9352 - 67
24LEULEULEULEU(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA95 - 9969 - 73
25LYSLYSGLYGLY(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA102 - 11876 - 92
26PHEPHELYSLYS(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA137 - 167111 - 141
27THRTHRGLNGLN(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA169 - 194143 - 168
28GLNGLNASPASP(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA197 - 227171 - 201
29PROPROLYSLYS(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA230 - 243204 - 217
210ASNASNSERSER(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA245 - 265219 - 239
211GLUGLUTHRTHR(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA267 - 282241 - 256
212ASPASPTHRTHR(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA285 - 286259 - 260
213ALAALAASPASP(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA288 - 308262 - 282
31GLYGLYSERSER(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC27 - 681 - 42
32ALAALAGLNGLN(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC71 - 7645 - 50
33ALAALAPROPRO(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC78 - 9352 - 67
34LEULEULEULEU(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC95 - 9969 - 73
35LYSLYSGLYGLY(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC102 - 11876 - 92
36PHEPHELYSLYS(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC137 - 167111 - 141
37THRTHRGLNGLN(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC169 - 194143 - 168
38GLNGLNASPASP(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC197 - 227171 - 201
39PROPROLYSLYS(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC230 - 243204 - 217
310ASNASNSERSER(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC245 - 265219 - 239
311GLUGLUTHRTHR(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC267 - 282241 - 256
312ASPASPTHRTHR(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC285 - 286259 - 260
313ALAALAASPASP(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC288 - 308262 - 282
41GLYGLYSERSER(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD27 - 681 - 42
42ALAALAGLNGLN(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD71 - 7645 - 50
43ALAALAPROPRO(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD78 - 9352 - 67
44LEULEULEULEU(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD95 - 9969 - 73
45LYSLYSGLYGLY(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD102 - 11876 - 92
46PHEPHELYSLYS(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD137 - 167111 - 141
47THRTHRGLNGLN(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD169 - 194143 - 168
48GLNGLNASPASP(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD197 - 227171 - 201
49PROPROLYSLYS(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD230 - 243204 - 217
410ASNASNSERSER(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD245 - 265219 - 239
411GLUGLUTHRTHR(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD267 - 282241 - 256
412ASPASPTHRTHR(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD285 - 286259 - 260
413ALAALAASPASP(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD288 - 308262 - 282

-
Components

#1: Protein
Zinc-binding lipoprotein AdcA


Mass: 33202.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Strain: ATCC BAA-255 / R6 / Gene: adcA, spr1975 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CWN2
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12.5% (w/v) polyethylene glycol 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) 2-methyl-2,4-pentanediol, 0.03 M MgCl2, 0.03 M CaCl2, 0.1 M imidazole-MES, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.03→19.36 Å / Num. obs: 68710 / % possible obs: 98.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 28.9744951541 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.108 / Net I/σ(I): 8.6
Reflection shellResolution: 2.03→2.1 Å / Rmerge(I) obs: 0.804 / Num. unique obs: 6809 / CC1/2: 0.66

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OSV
Resolution: 2.03→19.36 Å / SU ML: 0.233246804048 / Cross valid method: FREE R-VALUE / σ(F): 1.89478673062 / Phase error: 22.5871299159
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.212820796565 1999 2.90987961629 %
Rwork0.169005718258 66698 -
obs0.170294108042 68697 98.1582030692 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.10957472 Å2
Refinement stepCycle: LAST / Resolution: 2.03→19.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8352 0 4 462 8818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007405612004638504
X-RAY DIFFRACTIONf_angle_d0.9787315466211520
X-RAY DIFFRACTIONf_chiral_restr0.05672723030751320
X-RAY DIFFRACTIONf_plane_restr0.006510314078421476
X-RAY DIFFRACTIONf_dihedral_angle_d16.56781508315200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.10.3017213507491420.2542472875344709X-RAY DIFFRACTION97.00059988
2.0808-2.13690.3224890658521430.2308819395034771X-RAY DIFFRACTION97.5774424146
2.1369-2.19970.2557554448921410.2117649565614704X-RAY DIFFRACTION97.2696245734
2.1997-2.27060.291710375771410.2119476488924766X-RAY DIFFRACTION97.5546719682
2.2706-2.35170.24421716281420.2006910888074718X-RAY DIFFRACTION97.9049153908
2.3517-2.44560.2332194163521410.1881530383114737X-RAY DIFFRACTION97.8339350181
2.4456-2.55670.2266741007871430.1778673048844755X-RAY DIFFRACTION98.2744783307
2.5567-2.69120.2177543684671430.1753129008694752X-RAY DIFFRACTION98.1552035292
2.6912-2.85930.2377891829231440.1875209108924821X-RAY DIFFRACTION98.5314546537
2.8593-3.07920.2267558954121430.1774554740484782X-RAY DIFFRACTION98.6183420104
3.0792-3.38760.2112445187091440.1639871987354789X-RAY DIFFRACTION98.7785342411
3.3876-3.87440.1908129263681440.1506875374944770X-RAY DIFFRACTION98.8135934044
3.8744-4.86850.1710759883041440.1296986871214824X-RAY DIFFRACTION98.8656716418
4.8685-19.35830.175922869151440.1539621814814800X-RAY DIFFRACTION99.0583049489
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)
11.84248237495-0.6268715927020.4409726632490.848287768621-0.3949966225830.7555892131370.01099522500740.0632546422239-0.0775904682570.00296862958667-0.0532589079162-0.0947465303299-0.05197758999610.1343413256330.0004038310182240.1719159524740.002173874624910.02005408107530.1693584579750.007821726100350.189639339949-23.310494121890.856036469165.3532577361
21.436796603390.4109632102-0.201942943930.58087056068-0.1331316303530.6200812869870.0264562129404-0.0343048877044-0.103375669227-0.0153751513947-0.0004335644725470.06029362434630.0809655619638-0.04873033353435.44600338375E-50.1971802324270.005946668412860.001115283147750.1727084070120.003464623876160.183363865858-48.934776486687.874658639165.7888183887
30.114706028629-0.0290015719095-0.02719532856340.1624905897020.009841093552980.0293224690819-0.0123170363103-0.04643506964480.224633499353-0.01244245471110.0349104652697-0.0663611059598-0.389486246991-0.0155983711019-9.86988951664E-50.2855582390910.0790365755693-0.02293135890170.272504310025-0.03569070668730.350753737869-41.914309520863.600645562775.8514845829
40.1472010929470.007160494057760.007426111694990.124685198377-0.05476036380080.240752180566-0.00646518851133-0.7151787413020.2559525395280.06271311726080.138887048977-0.057954505546-0.08514949330020.13765603665-0.001117502262710.3382853922540.07058451175830.03937073942760.374111055882-0.0606552320070.329721724677-37.548990298859.596419334889.7465362264
50.2469290222130.0669286269234-0.08642587897450.1716765574930.09805231336040.356984430504-0.0118524173476-0.0171338002616-0.107316979577-0.07743034612-0.07434276200290.229996293033-0.0293558131883-0.149808909711-0.0002010420677410.2408502746150.0352049540183-0.0004163669971660.287971766992-0.04073282040860.376124955769-43.866528725251.323746492182.9009736014
60.103930817395-0.0573668465041-0.1203516481130.08470955179080.08131889793020.129050214746-0.144540891519-0.10216388489-0.09673861087160.0719591502211-0.04515719422720.0142518798749-0.0215290097043-0.004236424427661.43142930283E-50.2312050802490.009864008078890.04050823616510.1983680688810.004078471709040.267527383959-28.254592391746.623400624477.368388028
70.2416652945960.0035145289894-0.04723639299830.3270604718710.3261461776270.754454936260.1598040281070.360369753894-0.078991239126-0.34655515357-0.1844642240880.201318348241-0.189429563107-0.197309367656-0.004545299565770.2904729100950.057048180247-0.08527056635620.315140234401-0.03966825057240.261353088107-38.342948708657.02801173364.8287123517
80.5673344844390.0609567657265-0.1256462944960.1793280791320.05298283623060.0377590980781-0.00360926615134-0.107930641269-0.132174614228-0.0273105405863-0.0005279557956020.01127263671140.03639537791730.116200688037-8.4611583309E-50.1843358646930.009984372212550.01459895784780.1892975743590.002130417084490.164500862494-15.434268970252.069657723776.5498675436
90.402072888726-0.1052891908840.193368262110.05198040427950.05049165293940.3771372826720.0600228931452-0.3140141219260.201952490221-0.1037688672190.0556670299525-0.0255779313150.01901763870410.119284601136.25508857718E-50.2134206020320.004100279854030.01690326153640.290955190038-0.07932839114410.291153469506-5.9902275571157.337648261883.4476916959
100.0300904156096-0.0103497495495-0.02910489174420.443096341740.3626305911720.312339788516-0.060675464962-0.101095633570.223224312487-0.06279330163320.099502214704-0.0518223277447-0.1326539074040.0350513895180.0001301689148840.237402203972-0.01270566104340.01734652851210.195529291355-0.03483356416660.244215505345-19.958251811665.239223231879.1393171108
110.0668696813964-0.02584183102080.1069569241930.0937763672682-0.007545324111120.194444131339-0.02646488137970.3554299960930.579577891902-0.1753859205150.0486499013098-0.137640961655-0.1582174527930.03622798303880.002055919846540.27911894666-0.007794731044390.02101803872710.201881564062-0.002570817110910.228415117084-17.400577883960.762759207268.6423142053
120.987971142559-0.0669672047596-0.1063428158410.788810995559-0.4469846245240.506759270458-0.03011716904580.007491265982830.365680171474-0.0145291028055-0.111245533749-0.0321157201729-0.1233518067210.04714238073160.0006088605450910.257831693425-0.0420857057361-0.02295973560540.235684891420.02726950415560.2926008605977.3049504857264.934553935337.5738709585
130.0506559760125-0.0361152264011-0.0317546164360.097277618703-0.05042018338930.0654644123411-0.04196061777280.07415969934270.209630683258-0.297695877568-0.0877903412712-0.3458714545340.1217144128560.522285686622-0.002984233290460.272625681054-0.01714905986650.06522243111160.3446346115250.0694752268870.32245560659715.524063254860.206027982629.3374387591
140.2162544443630.216695781558-0.06132824673930.190789368581-0.05015424250870.0623407484664-0.122220689020.0889020042902-0.0508267830004-0.06810249417010.0185171197271-0.0407942216977-0.05431194024480.0333806188594-2.62290399725E-50.251466344251-0.0215582000486-0.007672518472980.219090321025-0.002505663821440.201673197392-2.9763780469651.73155381233.0513951933
150.1613262892010.173496005088-0.2303483941430.539917377363-0.3147472421770.3551614523430.0184915040862-0.343718818518-0.2568292989210.0689166065133-0.105891908304-0.1616511680830.001492522162330.1284532873695.69688759262E-50.194411540129-0.000660070783567-0.03077180135610.2146448193320.05126030126930.1924163885334.9625828195351.524050216848.7401341255
160.310092607610.0740020980977-0.05848628805290.1413113366550.09268792595770.0980794148504-0.114619189310.07554481979070.005941939319520.03229339936450.0800605341255-0.0870703834979-0.0518869688403-0.111362980415-0.0005737486080990.2086631970430.00426490192351-0.02076323101810.208372204733-0.006336076580750.209684809695-16.574120678251.567404053238.6506143261
170.179372702937-0.06640018611160.09232381486260.106422228960.008649394824720.0507097036958-0.01441966175560.833760716966-0.306733073138-0.2765047451170.13472903945-0.0167547655712-0.0573770381150.005756845388780.0003847065617550.4271853739410.018331398374-0.05918584028210.3530664837970.05354146061520.434949597327-27.009777763565.040208023729.2074968348
180.195905677188-0.1417386708780.01194887806820.20534880836-0.0559620991610.377893814745-0.0935132732087-0.205083205130.3757794762720.05626924744220.1194682960890.162144221878-0.208541951791-0.2572453099420.006138694258010.258999345820.0526860323213-0.0006429110140270.2042513043680.01304192045110.352818124704-25.649110606466.482392426937.9358744338
190.0808858781698-0.03248738628130.03852306068690.15682064659-0.2057202741340.2443799534230.0935400570012-0.0692375595160.4380907540530.2904827805580.02965964158420.10432802692-0.0651419246357-0.09967320364610.001750544139860.3356327174740.007360850103370.001856012469780.220792933896-0.04674263002080.337852514469-11.099825503667.628391203744.4562222217
200.0350486960289-0.0370429877237-0.01898587476730.0560612217598-0.06076296299130.2756385160010.065958862397-0.409252248250.08170121317510.168571878691-0.034768681530.0830260337066-0.184498695042-0.170184482319-2.92875695388E-60.2686813756870.02771796486810.007617677439150.211841377340.003118985575320.187812348042-15.925215455557.335259449648.0874082334
210.108800286045-0.06599779562790.1409466287680.189626177965-0.01290553253430.1727549498230.143326965469-0.132593031656-0.488267416448-0.0242906270079-0.146350784345-0.0559817007170.340923365868-0.007644727238920.0005518499533870.290447999226-0.0724610540790.01109833790510.267405156123-0.008413992811990.365147056162-32.022082072272.5308187882104.838530522
220.05662179906950.02383691732320.08033527274260.116013880127-0.05946853353160.242143518678-0.1417496214750.258343539995-0.356389718354-0.377889387883-0.0109537502828-0.00583652434760.00503581121518-0.06244892535910.0001190805451310.317485033997-0.0591436544207-0.02910925347330.430723779346-0.07877144294940.381811237904-28.331226771577.146994895690.9236318545
230.212240525445-0.160864934413-0.04067468443020.128262051083-0.0404882120690.376233518802-0.1662111723360.1382056436560.0573819396143-0.1820083818250.08329463219660.0630380756585-0.102695766438-0.242858050671-0.0002779031529620.259412394663-0.0251093764875-0.04893661814770.302303729067-0.02131612465320.292318163675-33.51544933385.003135926596.0003460131
240.15268274862-0.0148038268277-0.0222192146350.2282183176520.3034756198940.351606130581-0.0653639497858-0.0006585347206450.0399692777404-0.0192001953538-0.01956536910070.134207096334-0.115202225397-0.0392140292051-1.8420839933E-50.20612313928-0.0134110864724-0.02700363703950.233956394355-0.02561327870930.254800107346-25.681751887487.7755108655103.449232776
251.04025787949-0.3020984105560.08445660670720.6137947219060.07887795720610.4762526965880.0784445510146-0.5315935417650.05757249930120.31006726569-0.1477094764410.1476449372840.107720107631-0.226910383816-0.1960822148360.257468485956-0.07038754174810.08621354587870.340804792155-0.02152778214680.187330246251-28.249877314178.7338664059116.053401385
260.7142214087910.0189814215263-0.0920909820730.398919525196-0.004188864887230.206003763692-0.0154210462730.04440614590720.102559845977-0.01740194315740.0715948712839-0.0200896663713-0.03239429743780.0540492776066-0.0001297783327240.200737090864-0.0176022173411-0.01040254687940.210293060626-0.01522194973710.194537847312-5.4114460974184.1107597922104.175308646
270.0481035343323-0.0400000314199-0.03637218591160.03085238180640.02587328201450.02504146168140.1780952527360.4723311069840.3057226309910.02169284722680.05654109513210.05902256369250.05653215988110.1348045058980.003179265407230.267374867462-0.031153234327-0.002916188339130.409307100273-0.05258611293850.2501378574167.7383189228185.898872023495.5406095418
280.110331226120.047959569048-0.09938942847160.04294830470930.009970977393220.2038545819570.06003015729720.0208863402101-0.348665442448-0.135011470477-0.05471948282110.0264028701505-0.01779362258710.192082415039-6.6123825768E-50.235614288172-0.00280115887749-0.02049107312680.3320690432-0.03549954660850.2814208027592.2303753095974.966017673597.8628717232
290.110668902871-0.0764968143079-0.09279015718490.115240140023-0.1007773996660.3644635226810.06437879770950.0640684199662-0.1364943866380.05437486441440.04235179158460.1051993578210.2056797456850.112228208667-6.82062891055E-50.263175555562-0.0142672819561-0.02753752961590.2466056870240.004103957721970.249443118495-12.144882527570.157166648102.219137974
300.4157314244370.4935208915180.176841398830.6002680476360.1302058244020.3787133094090.069981144004-0.0117196292137-0.2328388085390.2159072887580.037241225206-0.2422125779070.2895783508990.2565302848260.03591784331860.2187687770310.0306969310601-0.01001279320610.1438958216070.0182386351280.149838341452-7.2983933673975.1939399304111.872602794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 27 through 192 )
2X-RAY DIFFRACTION2chain 'B' and (resid 193 through 309 )
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 54 )
4X-RAY DIFFRACTION4chain 'A' and (resid 55 through 76 )
5X-RAY DIFFRACTION5chain 'A' and (resid 77 through 113 )
6X-RAY DIFFRACTION6chain 'A' and (resid 114 through 144 )
7X-RAY DIFFRACTION7chain 'A' and (resid 145 through 192 )
8X-RAY DIFFRACTION8chain 'A' and (resid 193 through 231 )
9X-RAY DIFFRACTION9chain 'A' and (resid 232 through 266 )
10X-RAY DIFFRACTION10chain 'A' and (resid 267 through 291 )
11X-RAY DIFFRACTION11chain 'A' and (resid 292 through 309 )
12X-RAY DIFFRACTION12chain 'C' and (resid 27 through 91 )
13X-RAY DIFFRACTION13chain 'C' and (resid 92 through 108 )
14X-RAY DIFFRACTION14chain 'C' and (resid 109 through 144 )
15X-RAY DIFFRACTION15chain 'C' and (resid 145 through 192 )
16X-RAY DIFFRACTION16chain 'C' and (resid 193 through 220 )
17X-RAY DIFFRACTION17chain 'C' and (resid 221 through 244 )
18X-RAY DIFFRACTION18chain 'C' and (resid 245 through 268 )
19X-RAY DIFFRACTION19chain 'C' and (resid 269 through 291 )
20X-RAY DIFFRACTION20chain 'C' and (resid 292 through 309 )
21X-RAY DIFFRACTION21chain 'D' and (resid 27 through 54 )
22X-RAY DIFFRACTION22chain 'D' and (resid 55 through 76 )
23X-RAY DIFFRACTION23chain 'D' and (resid 77 through 101 )
24X-RAY DIFFRACTION24chain 'D' and (resid 102 through 144 )
25X-RAY DIFFRACTION25chain 'D' and (resid 145 through 192 )
26X-RAY DIFFRACTION26chain 'D' and (resid 193 through 231 )
27X-RAY DIFFRACTION27chain 'D' and (resid 232 through 245 )
28X-RAY DIFFRACTION28chain 'D' and (resid 246 through 268 )
29X-RAY DIFFRACTION29chain 'D' and (resid 269 through 291 )
30X-RAY DIFFRACTION30chain 'D' and (resid 292 through 309 )

+
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.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more