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- PDB-1q9w: S45-18 Fab pentasaccharide bisphosphate complex -

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Basic information

Entry
Database: PDB / ID: 1q9w
TitleS45-18 Fab pentasaccharide bisphosphate complex
Components(S45-18 Fab (IgG1k) ...) x 2
KeywordsIMMUNE SYSTEM / antigen-binding fragment / Fab / anti-cabohydrate / anti-LPS / antibody / immunoglobulin / Kdo / protein-carbohydrate complex
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / metal ion binding
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Igh protein / ENSMUSG00000076577 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNguyen, H.P. / Seto, N.O. / MacKenzie, C.R. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Germline antibody recognition of distinct carbohydrate epitopes.
Authors: Nguyen, H.P. / Seto, N.O. / MacKenzie, C.R. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V.
History
DepositionAug 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / 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.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The sequence of the protein was not deposited into any sequence database. Chains E and F ...SEQUENCE The sequence of the protein was not deposited into any sequence database. Chains E and F are bound ligands pentasaccharide bisphosphate alphaKdo-(2-4)-alphaKdo-(2-4)-alphaKdo -(2-6)-betaGlcN-4P-(1-6)-alphaGlcN-1P to Fab2. For the chain F only Kdo trisaccharide visible.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S45-18 Fab (IgG1k) light chain
B: S45-18 Fab (IgG1k) heavy chain
C: S45-18 Fab (IgG1k) light chain
D: S45-18 Fab (IgG1k) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,46411
Polymers97,5034
Non-polymers1,9617
Water13,818767
1
A: S45-18 Fab (IgG1k) light chain
B: S45-18 Fab (IgG1k) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9856
Polymers48,7512
Non-polymers1,2344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-36 kcal/mol
Surface area19660 Å2
MethodPISA
2
C: S45-18 Fab (IgG1k) light chain
D: S45-18 Fab (IgG1k) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4795
Polymers48,7512
Non-polymers7273
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-39 kcal/mol
Surface area19380 Å2
MethodPISA
3
A: S45-18 Fab (IgG1k) light chain
B: S45-18 Fab (IgG1k) heavy chain
hetero molecules

C: S45-18 Fab (IgG1k) light chain
D: S45-18 Fab (IgG1k) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,46411
Polymers97,5034
Non-polymers1,9617
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+3/2,-y+2,z+1/21
Buried area12630 Å2
ΔGint-88 kcal/mol
Surface area37750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.200, 113.900, 133.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody S45-18 Fab (IgG1k) light chain


Mass: 24306.039 Da / Num. of mol.: 2 / Fragment: Fab1 Light chain kappa / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q52L64*PLUS
#2: Antibody S45-18 Fab (IgG1k) heavy chain


Mass: 24445.398 Da / Num. of mol.: 2 / Fragment: Fab1 Heavy chain g1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: I6L985*PLUS

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Sugars , 2 types, 2 molecules

#3: Polysaccharide 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1160.817 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,5,4/[a2122h-1a_1-5_1*OPO/3O/3=O_2*N][a2122h-1a_1-5_2*N_4*OPO/3O/3=O][Aad1122h-2a_2-6]/1-2-3-3-3/a6-b1_b6-c2_c4-d2_d4-e2WURCSPDB2Glycan 1.1.0
[][P]{[(0+1)][a-D-GlcpN]{[(6+1)][b-D-GlcpN]{[(4+0)][P]{}[(6+2)][a-D-Kdop]{[(4+2)][a-D-Kdop]{[(4+2)][a-D-Kdop]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid


Type: oligosaccharide / Mass: 678.546 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DKdopa2-4DKdopa2-4DKdopa2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[Aad1122h-2a_2-6]/1-1-1/a4-b2_b4-c2WURCSPDB2Glycan 1.1.0
[][a-D-Kdop]{[(4+2)][a-D-Kdop]{[(4+2)][a-D-Kdop]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 772 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: pentasaccharide, magnesium chloride, PEG 4000, tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: Nguyen, H.P., (2001) Acta Cryst., D57, 1872.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
19 mg/mlFab1dropwith pentasaccharide bisphosphate antigen
20.13 M1dropMgCl2
313 %(w/v)PEG40001drop
467 mMTris1droppH8.5
50.2 M1reservoirMgCl2
620 %(w/v)PEG40001reservoir
70.1 MTris1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.15 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 21, 2001 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 1.75→19.9 Å / Num. all: 106072 / Num. obs: 99720 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.4 Å2 / Limit h max: 39 / Limit h min: 0 / Limit k max: 65 / Limit k min: 0 / Limit l max: 76 / Limit l min: 0 / Observed criterion F max: 450248.69 / Observed criterion F min: 0.32
Reflection shellResolution: 1.75→1.81 Å / % possible all: 93.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 106111 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Num. measured all: 406104 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 93.1 % / Num. unique obs: 10237 / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1q9o, S45-18 Fab unliganded

1q9o


Resolution: 1.75→19.9 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 9994 10 %random
Rwork0.212 ---
obs-99720 90.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 53.4188 Å2 / ksol: 0.362688 e/Å3
Displacement parametersBiso max: 79.03 Å2 / Biso mean: 30.56 Å2 / Biso min: 12.49 Å2
Baniso -1Baniso -2Baniso -3
1--3.24 Å20 Å20 Å2
2---4.3 Å20 Å2
3---7.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Luzzati d res high-1.75
Refinement stepCycle: LAST / Resolution: 1.75→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6850 0 127 767 7744
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_torsion_deg26.8
X-RAY DIFFRACTIONc_torsion_impr_deg1.04
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.75-1.810.33687810.40.30975770.01110945845577.2
1.81-1.880.318860100.28777110.01110927857178.4
1.88-1.970.2829319.80.23685600.00910960949186.6
1.97-2.070.2559799.90.2288680.00810925984790.1
2.07-2.20.257104810.20.21692600.008109701030894
2.2-2.370.252110210.40.21395060.008110031060896.4
2.37-2.610.265109910.30.22595820.008109831068197.3
2.61-2.990.26410359.60.22597020.008110571073797.1
2.99-3.760.2410529.80.20896290.007111291068196
3.76-19.90.21110109.80.18293310.007114711034190.1
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.paramwater.top
X-RAY DIFFRACTION5kdo6.parkdo6.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.009

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