[English] 日本語
Yorodumi
- PDB-2jb6: Fab fragment in complex with small molecule hapten, crystal form-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jb6
TitleFab fragment in complex with small molecule hapten, crystal form-2
Components
  • FAB FRAGMENT MOR03268 HEAVY CHAIN
  • FAB FRAGMENT MOR03268 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / CDR / TSC / FAB / HUCAL / FLUORESCENT DYE / IMMUNOGLOBULIN DOMAIN / ANTIBODY FRAGMENT / DIAGNOSTIC IMAGING
Function / homology
Function and homology information


IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / antigen binding / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins ...: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-T5C / Immunoglobulin lambda constant 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsHillig, R.C. / Baesler, S. / Malawski, G. / Badock, V. / Bahr, I. / Schirner, M. / Licha, K.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Fab Mor03268 Triggers Absorption Shift of a Diagnostic Dye Via Packaging in a Solvent-Shielded Fab Dimer Interface
Authors: Hillig, R.C. / Urlinger, S. / Fanghanel, J. / Brocks, B. / Haenel, C. / Stark, Y. / Sulzle, D. / Svergun, D.I. / Baesler, S. / Malawski, G. / Moosmayer, D. / Menrad, A. / Schirner, M. / Licha, K.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization and Molecular-Replacement Solution of a Diagnostic Fluorescent Dye in Complex with a Specific Fab Fragment.
Authors: Hillig, R.C. / Baesler, S. / Urlinger, S. / Stark, Y. / Bauer, S. / Badock, V. / Huber, M. / Bahr, I. / Schirner, M. / Licha, K.
History
DepositionDec 3, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FAB FRAGMENT MOR03268 LIGHT CHAIN
B: FAB FRAGMENT MOR03268 HEAVY CHAIN
H: FAB FRAGMENT MOR03268 HEAVY CHAIN
L: FAB FRAGMENT MOR03268 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7106
Polymers98,1674
Non-polymers1,5442
Water32418
1
A: FAB FRAGMENT MOR03268 LIGHT CHAIN
B: FAB FRAGMENT MOR03268 HEAVY CHAIN
hetero molecules

A: FAB FRAGMENT MOR03268 LIGHT CHAIN
B: FAB FRAGMENT MOR03268 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7106
Polymers98,1674
Non-polymers1,5442
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area10420 Å2
ΔGint-63.2 kcal/mol
Surface area44370 Å2
MethodPQS
2
H: FAB FRAGMENT MOR03268 HEAVY CHAIN
L: FAB FRAGMENT MOR03268 LIGHT CHAIN
hetero molecules

H: FAB FRAGMENT MOR03268 HEAVY CHAIN
L: FAB FRAGMENT MOR03268 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7106
Polymers98,1674
Non-polymers1,5442
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area10520 Å2
ΔGint-60.8 kcal/mol
Surface area44820 Å2
MethodPQS
Unit cell
Length a, b, c (Å)77.028, 77.028, 379.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-1222-

T5C

21B-1222-

T5C

31H-1222-

T5C

41H-1222-

T5C

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21A
12H
22B
13B
23H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUTHRTHR5LD4 - 54 - 5
211LEULEUTHRTHR5AA4 - 54 - 5
121GLNGLNSERSER2LD6 - 96 - 9
221GLNGLNSERSER2AA6 - 96 - 9
131VALVALPROPRO5LD10 - 1410 - 14
231VALVALPROPRO5AA10 - 1410 - 14
141GLYGLYGLYGLY6LD1515
241GLYGLYGLYGLY6AA1515
151GLNGLNSERSER5LD16 - 2116 - 21
251GLNGLNSERSER5AA16 - 2116 - 21
161CYSCYSGLYGLY2LD22 - 2422 - 24
261CYSCYSGLYGLY2AA22 - 2422 - 24
171THRTHRASNASN6LD25 - 3325 - 33
271THRTHRASNASN6AA25 - 3325 - 33
181TYRTYRGLNGLN2LD34 - 3934 - 39
281TYRTYRGLNGLN2AA34 - 3934 - 39
191GLNGLNGLNGLN5LD4040
291GLNGLNGLNGLN5AA4040
1101HISHISALAALA6LD41 - 4541 - 45
2101HISHISALAALA6AA41 - 4541 - 45
1111PROPROPHEPHE2LD46 - 6446 - 64
2111PROPROPHEPHE2AA46 - 6446 - 64
1121SERSERLYSLYS6LD65 - 6865 - 68
2121SERSERLYSLYS6AA65 - 6865 - 68
1131SERSERILEILE2LD69 - 7769 - 77
2131SERSERILEILE2AA69 - 7769 - 77
1141SERSERLEULEU6LD78 - 8078 - 80
2141SERSERLEULEU6AA78 - 8078 - 80
1151GLNGLNSERSER2LD81 - 9281 - 92
2151GLNGLNSERSER2AA81 - 9281 - 92
1161TRPTRPASNASN5LD93 - 9693 - 96
2161TRPTRPASNASN5AA93 - 9693 - 96
1171LEULEUTHRTHR6LD97 - 10697 - 106
2171LEULEUTHRTHR6AA97 - 10697 - 106
1181LYSLYSLYSLYS5LD107107
2181LYSLYSLYSLYS5AA107107
1191LEULEUPROPRO2LD108 - 125108 - 125
2191LEULEUPROPRO2AA108 - 125108 - 125
1201SERSERSERSER6LD126 - 127126 - 127
2201SERSERSERSER6AA126 - 127126 - 127
1211GLUGLUGLUGLU2LD128 - 129128 - 129
2211GLUGLUGLUGLU2AA128 - 129128 - 129
1221LEULEULYSLYS6LD130 - 134130 - 134
2221LEULEULYSLYS6AA130 - 134130 - 134
1231ALAALAILEILE2LD135 - 141135 - 141
2231ALAALAILEILE2AA135 - 141135 - 141
1241SERSERASPASP6LD142 - 143142 - 143
2241SERSERASPASP6AA142 - 143142 - 143
1251PHEPHEPHEPHE2LD144144
2251PHEPHEPHEPHE2AA144144
1261TYRTYRTHRTHR5LD145 - 150145 - 150
2261TYRTYRTHRTHR5AA145 - 150145 - 150
1271VALVALTRPTRP2LD151 - 153151 - 153
2271VALVALTRPTRP2AA151 - 153151 - 153
1281LYSLYSVALVAL6LD154 - 164154 - 164
2281LYSLYSVALVAL6AA154 - 164154 - 164
1291GLUGLUPROPRO2LD165 - 169165 - 169
2291GLUGLUPROPRO2AA165 - 169165 - 169
1301SERSERASNASN5LD170 - 175170 - 175
2301SERSERASNASN5AA170 - 175170 - 175
1311LYSLYSLEULEU2LD176 - 183176 - 183
2311LYSLYSLEULEU2AA176 - 183176 - 183
1321SERSERGLUGLU5LD184 - 188184 - 188
2321SERSERGLUGLU5AA184 - 188184 - 188
1331GLNGLNTRPTRP2LD189 - 190189 - 190
2331GLNGLNTRPTRP2AA189 - 190189 - 190
1341LYSLYSSERSER5LD191 - 192191 - 192
2341LYSLYSSERSER5AA191 - 192191 - 192
1351HISHISARGARG6LD193 - 194193 - 194
2351HISHISARGARG6AA193 - 194193 - 194
1361SERSERTHRTHR5LD195 - 201195 - 201
2361SERSERTHRTHR5AA195 - 201195 - 201
1371HISHISTHRTHR2LD202 - 206202 - 206
2371HISHISTHRTHR2AA202 - 206202 - 206
1381VALVALPROPRO5LD207 - 213207 - 213
2381VALVALPROPRO5AA207 - 213207 - 213
112VALVALGLYGLY6HC5 - 85 - 8
212VALVALGLYGLY6BB5 - 85 - 8
122ALAALALYSLYS3HC9 - 129 - 12
222ALAALALYSLYS3BB9 - 129 - 12
132LYSLYSSERSER6HC13 - 1713 - 17
232LYSLYSSERSER6BB13 - 1713 - 17
142VALVALVALVAL2HC1818
242VALVALVALVAL2BB1818
152LYSLYSVALVAL5HC19 - 2019 - 20
252LYSLYSVALVAL5BB19 - 2019 - 20
162SERSERALAALA6HC21 - 2421 - 24
262SERSERALAALA6BB21 - 2421 - 24
172TYRTYRTYRTYR6HC3232
272TYRTYRTYRTYR6BB3232
182ALAALAVALVAL5HC33 - 3733 - 37
282ALAALAVALVAL5BB33 - 3733 - 37
192ARGARGALAALA2HC38 - 4038 - 40
292ARGARGALAALA2BB38 - 4038 - 40
1102PROPROPROPRO5HC41 - 5341 - 53
2102PROPROPROPRO5BB41 - 5341 - 53
1112TYRTYRLYSLYS6HC54 - 6354 - 63
2112TYRTYRLYSLYS6BB54 - 6354 - 63
1122VALVALTHRTHR6HC68 - 7868 - 78
2122VALVALTHRTHR6BB68 - 7868 - 78
1132ALAALALEULEU2HC79 - 8379 - 83
2132ALAALALEULEU2BB79 - 8379 - 83
1142SERSERGLUGLU6HC84 - 8984 - 89
2142SERSERGLUGLU6BB84 - 8984 - 89
1152ASPASPMETMET2HC90 - 10190 - 101
2152ASPASPMETMET2BB90 - 10190 - 101
1162SERSERHISHIS5HC102 - 105102 - 105
2162SERSERHISHIS5BB102 - 105102 - 105
1172LEULEUVALVAL2HC106 - 118106 - 118
2172LEULEUVALVAL2BB106 - 118106 - 118
1182SERSERSERSER5HC119 - 122119 - 122
2182SERSERSERSER5BB119 - 122119 - 122
1192THRTHRALAALA2HC123 - 132123 - 132
2192THRTHRALAALA2BB123 - 132123 - 132
1202PROPROPROPRO6HC133133
2202PROPROPROPRO6BB133133
1212ALAALAASNASN2HC144 - 162144 - 162
2212ALAALAASNASN2BB144 - 162144 - 162
1222SERSERTHRTHR6HC163 - 167163 - 167
2222SERSERTHRTHR6BB163 - 167163 - 167
1232SERSERHISHIS5HC168 - 171168 - 171
2232SERSERHISHIS5BB168 - 171168 - 171
1242THRTHRSERSER2HC172 - 187172 - 187
2242THRTHRSERSER2BB172 - 187172 - 187
1252VALVALLEULEU5HC188 - 196188 - 196
2252VALVALLEULEU5BB188 - 196188 - 196
1262GLYGLYGLNGLN6HC197 - 199197 - 199
2262GLYGLYGLNGLN6BB197 - 199197 - 199
1272THRTHRTHRTHR5HC200200
2272THRTHRTHRTHR5BB200200
1282TYRTYRCYSCYS2HC201 - 203201 - 203
2282TYRTYRCYSCYS2BB201 - 203201 - 203
1292ASNASNVALVAL5HC204 - 205204 - 205
2292ASNASNVALVAL5BB204 - 205204 - 205
1302ASNASNVALVAL2HC206 - 218206 - 218
2302ASNASNVALVAL2BB206 - 218206 - 218
1312GLUGLUGLUGLU6HC219219
2312GLUGLUGLUGLU6BB219219
1322GLYGLYALAALA6HC140 - 143140 - 143
2322GLYGLYALAALA6BB140 - 143140 - 143
113T5CT5CT5CT5C1BE1222
213T5CT5CT5CT5C1HF1222

NCS ensembles :
ID
1
2
3
/ NCS oper:
IDCode
1given
2given
3given

-
Components

#1: Antibody FAB FRAGMENT MOR03268 LIGHT CHAIN


Mass: 22754.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: IN VITRO SELECTED FROM A LIBRARY AND OPTIMIZED IN SEVERAL MATURATION STEPS
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0DOY3*PLUS
#2: Antibody FAB FRAGMENT MOR03268 HEAVY CHAIN


Mass: 26328.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: IN VITRO SELECTED FROM A LIBRARY AND OPTIMIZED IN SEVERAL MATURATION STEPS
Production host: ESCHERICHIA COLI (E. coli)
#3: Chemical ChemComp-T5C / 2-{(1E,3Z,5E,7E)-7-[3,3-DIMETHYL-5-SULFO-1-(2-SULFOETHYL)-1,3-DIHYDRO-2H-INDOL-2-YLIDENE]-4-METHYLHEPTA-1,3,5-TRIEN-1-YL}-3,3-DIMETHYL-5-SULFO-1-(2-SULFOETHYL)-3H-INDOLIUM / TETRASULFOCYANINE


Mass: 771.918 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H39N2O12S4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFAB FRAGMENT SELECTED IN VITRO FROM A LIBRARY, AND OPTIMIZED FURTHER BY MATURATION STEPS. THIS ...FAB FRAGMENT SELECTED IN VITRO FROM A LIBRARY, AND OPTIMIZED FURTHER BY MATURATION STEPS. THIS HEAVY CHAIN HAS A C-TERMINAL MYC-HIS6 TAG (RESIDUES 222-244)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 4
Details: 2.6-2.7M AMMONIUM SULPHATE, 5% PEG400, 0.1M SODIUM CITRATE PH 4. ADDITIONAL 10% GLYCEROL AS CRYO BUFFER.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.85→48.9 Å / Num. obs: 27756 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 72.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.6
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.5 / % possible all: 78.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JB5

2jb5


Resolution: 2.85→47.4 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.879 / SU B: 35.394 / SU ML: 0.314 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 2.381 / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE LOOP REGIONS H64-67, B65-66 AND B134 - 139 WERE MODELLED, BUT WERE NOT VERY WELL ORDERED IN THE DENSITY. FOR BOTH FAB MOLECULES IN THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE LOOP REGIONS H64-67, B65-66 AND B134 - 139 WERE MODELLED, BUT WERE NOT VERY WELL ORDERED IN THE DENSITY. FOR BOTH FAB MOLECULES IN THE ASYMMETRIC UNIT, THE SYMMETRIC LIGAND IS BOUND BETWEEN THE RESPECTIVE FAB AND ONE OF ITS SYMMETRY MATES IN A FAB DIMER INTERFACE. THE LIGAND IS THUS SIMULTAENOUSLY COORDINATED BY THE ANTIGEN BINDING SITES OF BOTH FABS. IT IS ITSELF LOCATED ON THE TWOFOLD CRYSTALLOGRAPHIC SYMMETRY AXIS. THIS WAS TAKEN INTO ACCOUNT DURING REFINEMENT BY REFINING IT WITH AN OCCUPANY OF 0.5.
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1427 5.2 %RANDOM
Rwork0.229 ---
obs0.231 26266 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.85→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6323 0 100 18 6441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226591
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.979015
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3345840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32624.701234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.74115999
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6421516
X-RAY DIFFRACTIONr_chiral_restr0.0840.21004
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024964
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.22653
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24348
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.2104
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3861.54270
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.71526801
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.81232868
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3884.52214
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11L416tight positional0.030.05
12A416tight positional0.030.05
21H396tight positional0.040.05
22B396tight positional0.040.05
31B50tight positional0.010.05
32H50tight positional0.010.05
11L592medium positional0.30.5
12A592medium positional0.30.5
21H542medium positional0.250.5
22B542medium positional0.250.5
11L550loose positional0.395
12A550loose positional0.395
21H552loose positional0.575
22B552loose positional0.575
11L416tight thermal0.050.5
12A416tight thermal0.050.5
21H396tight thermal0.060.5
22B396tight thermal0.060.5
31B50tight thermal0.020.5
32H50tight thermal0.020.5
11L592medium thermal0.312
12A592medium thermal0.312
21H542medium thermal0.32
22B542medium thermal0.32
11L550loose thermal0.9310
12A550loose thermal0.9310
21H552loose thermal0.7610
22B552loose thermal0.7610
LS refinement shellResolution: 2.85→2.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 105 -
Rwork0.31 1688 -
obs--89.61 %
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)
17.873-1.60030.47552.37910.3261.9746-0.0336-0.54890.49260.22980.1256-0.1844-0.03680.0452-0.0921-0.383-0.0542-0.011-0.223-0.0632-0.122264.19621.684143.393
25.5317-0.8879-0.49872.0726-0.16131.8980.0335-0.511-0.09480.23540.0610.22240.0306-0.1136-0.0946-0.3819-0.0249-0.0171-0.22590.0276-0.181290.15-16.05143.395
33.1401-0.6579-1.19071.51470.97455.47910.06840.457-0.0198-0.3452-0.35910.4407-0.1083-1.30720.29060.23250.1964-0.07130.2976-0.12660.03958.09512.395110.698
43.3914-0.03261.87421.1456-0.46146.03820.05810.4531-0.0438-0.287-0.0787-0.23440.08841.04480.02060.05740.04070.0120.0719-0.0098-0.128194.612-8.99110.341
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H121 - 220
2X-RAY DIFFRACTION1L113 - 213
3X-RAY DIFFRACTION2B121 - 220
4X-RAY DIFFRACTION2A113 - 213
5X-RAY DIFFRACTION3H3 - 120
6X-RAY DIFFRACTION3L4 - 112
7X-RAY DIFFRACTION3B1222
8X-RAY DIFFRACTION4B4 - 120
9X-RAY DIFFRACTION4A3 - 112
10X-RAY DIFFRACTION4H1222

+
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://pdbjlc1.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