[English] 日本語
Yorodumi
- PDB-3nn8: Crystal structure of engineered antibody fragment based on 3D5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nn8
TitleCrystal structure of engineered antibody fragment based on 3D5
ComponentsEngineered scFv
KeywordsIMMUNE SYSTEM / beta barrel / antibody fragment / immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsLieberman, R.L. / Maynard, J.A. / Drury, J.E. / Pai, J. / Culver, J.A.
CitationJournal: To be Published
Title: Peptide-binding single chain Antibody fragment (SCFV) chaperones for protein co-crystallization
Authors: Pai, J. / Culver, J.A. / Drury, J.E. / Lieberman, R.L. / Maynard, J.A.
History
DepositionJun 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Mar 27, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine_ls_restr_ncs / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_sheet_range
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.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_peptide_omega.auth_asym_id_1 / _pdbx_validate_peptide_omega.auth_asym_id_2 / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine_ls_restr_ncs.pdbx_auth_asym_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.auth_comp_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.label_comp_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_auth_comp_id_2 / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_mon_prot_cis.pdbx_label_comp_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ncs_dom.details / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_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_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_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_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Engineered scFv
B: Engineered scFv
C: Engineered scFv
D: Engineered scFv


Theoretical massNumber of molelcules
Total (without water)108,5564
Polymers108,5564
Non-polymers00
Water0
1
A: Engineered scFv


Theoretical massNumber of molelcules
Total (without water)27,1391
Polymers27,1391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-14 kcal/mol
Surface area10340 Å2
MethodPISA
2
B: Engineered scFv


Theoretical massNumber of molelcules
Total (without water)27,1391
Polymers27,1391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-13 kcal/mol
Surface area10430 Å2
MethodPISA
3
C: Engineered scFv


Theoretical massNumber of molelcules
Total (without water)27,1391
Polymers27,1391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-13 kcal/mol
Surface area10390 Å2
MethodPISA
4
D: Engineered scFv


Theoretical massNumber of molelcules
Total (without water)27,1391
Polymers27,1391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-14 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)266.637, 266.637, 266.637
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13A
23B
14C
24D

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNSERSERAA116 - 236135 - 255
21GLNGLNSERSERBB116 - 236135 - 255
12GLNGLNSERSERCC116 - 236135 - 255
22GLNGLNSERSERDD116 - 236135 - 255
13ASPASPSERSERAA1 - 1222 - 141
23ASPASPSERSERBB1 - 1222 - 141
14ASPASPGLYGLYCC1 - 1152 - 116
24ASPASPGLYGLYDD1 - 1152 - 116

NCS ensembles :
ID
1
2
3
4
DetailsThere are 4 biological units in the asymmetric unit (chains A & B, chains C & F, chains D & E, chains G & H)

-
Components

#1: Antibody
Engineered scFv


Mass: 27139.096 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, magnesium acetate, pH 6.5, vapor diffusion, hanging drop, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRedundancy: 5.6 % / Av σ(I) over netI: 5.6 / Number: 158332 / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / D res high: 3.1 Å / D res low: 154.303 Å / Num. obs: 28384 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
9.819.9387.810.0430.0435.4
6.939.810010.0570.0575.5
5.666.9310010.0850.0855.6
4.95.6610010.0840.0845.6
4.384.910010.0820.0825.6
44.3810010.0880.0885.6
3.71410010.1370.1375.6
3.473.7110010.1780.1785.6
3.273.4710010.2240.2245.6
3.13.2710010.3420.3425.6
ReflectionResolution: 3.1→154.303 Å / Num. all: 28384 / Num. obs: 28384 / % possible obs: 99.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.1-3.275.60.3422.12295541340.342100
3.27-3.475.60.2243.22179738960.224100
3.47-3.715.60.17842064436810.178100
3.71-45.60.1375.21920834210.137100
4-4.385.60.0887.91777231730.088100
4.38-4.95.60.0828.51605728660.082100
4.9-5.665.60.0848.41409725240.084100
5.66-6.935.60.0858.31209921740.085100
6.93-9.85.50.05711.6926216850.057100
9.8-19.9285.40.04314.144418300.04387.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.19 Å19.88 Å
Translation3.19 Å19.88 Å

-
Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KTR

1ktr


Resolution: 3.1→154.3 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.875 / WRfactor Rfree: 0.2196 / WRfactor Rwork: 0.1673 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8443 / SU B: 33.974 / SU ML: 0.282 / SU R Cruickshank DPI: 0.321 / SU Rfree: 0.3905 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 1439 5.1 %RANDOM
Rwork0.1831 ---
obs0.1858 28371 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 190.15 Å2 / Biso mean: 69.6674 Å2 / Biso min: 13.85 Å2
Refinement stepCycle: LAST / Resolution: 3.1→154.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7272 0 0 0 7272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227444
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.95910086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2685939
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67323.649296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.12151241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7431540
X-RAY DIFFRACTIONr_chiral_restr0.1090.21095
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215584
X-RAY DIFFRACTIONr_mcbond_it0.4551.54675
X-RAY DIFFRACTIONr_mcangle_it0.9327524
X-RAY DIFFRACTIONr_scbond_it1.34432769
X-RAY DIFFRACTIONr_scangle_it2.2954.52562
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A938MEDIUM POSITIONAL0.260.5
1A938MEDIUM THERMAL0.312
2C938MEDIUM POSITIONAL0.270.5
2C938MEDIUM THERMAL0.312
3A874MEDIUM POSITIONAL0.420.5
3A874MEDIUM THERMAL0.372
4C883MEDIUM POSITIONAL0.490.5
4C883MEDIUM THERMAL0.392
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 99 -
Rwork0.251 1961 -
all-2060 -
obs--99.95 %
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)
16.78741.01531.78434.14921.46846.4684-0.03580.09040.23270.09960.0866-0.3080.0665-0.5396-0.05070.05690.02690.0110.08080.00250.1292-22.482-51.9011.147
24.7104-4.48180.23418.11560.92075.8984-0.3507-0.66960.07470.80450.23070.10120.0269-0.60250.120.18230.1314-0.0480.3591-0.09370.1596-33.515-41.2715.445
34.2158-0.68661.36196.6399-1.39567.3893-0.0056-0.0836-0.2449-0.05520.0283-0.3305-0.5278-0.0209-0.02270.0604-0.02440.01130.0376-0.0250.1459-51.882-110.8131.172
45.52130.90930.54676.5841-1.72526.242-0.1449-0.04070.23020.03570.1356-0.14850.4161-0.01710.00930.05860.0555-0.02570.1503-0.05270.0388-56.054-20.609-0.013
59.0767-6.0361-0.32068.1794-0.58574.12590.74221.2327-0.1172-0.9724-0.8427-0.09740.20220.00410.10050.36660.24280.05370.35270.05840.0707-44.293-29.897-14.574
68.89094.65730.60855.5146-0.54495.47650.2867-0.81420.11190.6468-0.4457-0.0767-0.60110.06550.15890.3454-0.1366-0.08020.23310.05910.1387-41.305-99.78615.454
77.32670.222-2.16175.3757-0.3026.35070.0512-0.1037-0.14250.0518-0.1829-0.29210.0916-0.48860.13170.1276-0.0581-0.03750.07290.01740.0292-20.615-77.244-0.032
88.03626.3314-1.44510.0422-0.08495.0103-0.85271.0771-0.1652-1.12370.81250.02840.0403-0.29310.04020.3103-0.23020.02220.3481-0.03510.0904-29.906-88.988-14.583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A116 - 230
2X-RAY DIFFRACTION2A1 - 115
3X-RAY DIFFRACTION3B116 - 230
4X-RAY DIFFRACTION4C116 - 230
5X-RAY DIFFRACTION5C1 - 115
6X-RAY DIFFRACTION6B1 - 115
7X-RAY DIFFRACTION7D116 - 230
8X-RAY DIFFRACTION8D1 - 115

+
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