[English] 日本語
Yorodumi
- PDB-1q9l: S25-2 Fab Unliganded 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1q9l
TitleS25-2 Fab Unliganded 2
Components
  • S25-2 Fab (IgG1k) heavy chain
  • S25-2 Fab (IgG1k) light chain
KeywordsIMMUNE SYSTEM / antigen-binding fragment / Fab / anti-carbohydrate / anti-LPS / antibody / immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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 25, 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 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The sequence of the protein was not deposited into any sequence database.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: S25-2 Fab (IgG1k) heavy chain
D: S25-2 Fab (IgG1k) heavy chain
A: S25-2 Fab (IgG1k) light chain
C: S25-2 Fab (IgG1k) light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,07414
Polymers96,7084
Non-polymers36610
Water7,188399
1
B: S25-2 Fab (IgG1k) heavy chain
A: S25-2 Fab (IgG1k) light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4685
Polymers48,3542
Non-polymers1143
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-78 kcal/mol
Surface area19640 Å2
MethodPISA
2
D: S25-2 Fab (IgG1k) heavy chain
C: S25-2 Fab (IgG1k) light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6069
Polymers48,3542
Non-polymers2527
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-89 kcal/mol
Surface area19560 Å2
MethodPISA
3
D: S25-2 Fab (IgG1k) heavy chain
C: S25-2 Fab (IgG1k) light chain
hetero molecules

B: S25-2 Fab (IgG1k) heavy chain
A: S25-2 Fab (IgG1k) light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,07414
Polymers96,7084
Non-polymers36610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_458x-1/2,-y+1/2,-z+31
Buried area10590 Å2
ΔGint-202 kcal/mol
Surface area37460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.700, 96.000, 114.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody S25-2 Fab (IgG1k) heavy chain


Mass: 24110.967 Da / Num. of mol.: 2 / Fragment: Fab Heavy chain g1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody S25-2 Fab (IgG1k) light chain


Mass: 24242.898 Da / Num. of mol.: 2 / Fragment: Fab Light chain kappa / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: zinc acetate, magnesium chloride, PEG 8000, PEG 4000, cacodylate, tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
118 mg/mlFab1drop
240 mM1dropMgCl2
330 mM1dropZnCl2
48 %(w/v)PEG40001drop
511 %(w/v)ethylene glycol1drop
620 mMTris1droppH8
7200 mMTris1reservoir
825 %(w/v)1reservoirMgCl2
9100 mMPEG40001reservoirpH8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.15 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 17, 2002 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.28→19.85 Å / Num. all: 38051 / Num. obs: 36566 / % possible obs: 84.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.9 Å2 / Limit h max: 37 / Limit h min: 0 / Limit k max: 41 / Limit k min: 0 / Limit l max: 49 / Limit l min: 0 / Observed criterion F max: 281431.24 / Observed criterion F min: 0.32
Reflection shellResolution: 2.28→2.36 Å / % possible all: 77.5
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 38076 / % possible obs: 88.4 % / Observed criterion σ(F): 0 / Num. measured all: 230670 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 77.5 % / Num. unique obs: 3282 / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.2

-
Processing

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

1q9o


Resolution: 2.28→19.85 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 3663 10 %random
Rwork0.216 ---
all-43071 --
obs-36566 84.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 36.2856 Å2 / ksol: 0.298489 e/Å3
Displacement parametersBiso max: 100.63 Å2 / Biso mean: 40.33 Å2 / Biso min: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1-13.78 Å20 Å20 Å2
2---7.16 Å20 Å2
3----6.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.27 Å
Luzzati d res high-2.28
Refinement stepCycle: LAST / Resolution: 2.28→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6798 0 10 399 7207
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_torsion_deg27
X-RAY DIFFRACTIONc_torsion_impr_deg0.91
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 (%)
2.28-2.360.34529910.20.28526360.024243293569.2
2.36-2.460.37131010.30.27727010.0214248301170.9
2.46-2.570.343139.80.2628890.0194283320274.8
2.57-2.70.35134210.40.25229620.0194235330478
2.7-2.870.335351100.24631480.0184281349981.7
2.87-3.090.3123679.90.22533240.0164300369185.8
3.09-3.40.3043869.60.22436170.0154290400393.3
3.4-3.890.27943810.30.21137970.0134342423597.5
3.89-4.890.2494279.90.18738670.0124357429498.6
4.89-19.850.2824309.80.22439620.0144529439297
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.paramwater.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.287
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.009

+
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://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