[English] 日本語
Yorodumi
- PDB-4pub: Crystal structure of Fab DX-2930 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pub
TitleCrystal structure of Fab DX-2930
Components
  • DX-2930 HEAVY CHAIN
  • DX-2930 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / FAB / ANTIBODY / KALLIKREIN / BLOOD / PLASMA / PLASMA KALLIKREIN-MEDIATED EDEMA / ACUTE HEREDITARY ANGIOEDEMA / HAE
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / immune response / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
Ig-like domain-containing protein / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsAbendroth, J. / Edwards, T.E. / Nixon, A. / Ladner, R.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Inhibition of plasma kallikrein by a highly specific active site blocking antibody.
Authors: Kenniston, J.A. / Faucette, R.R. / Martik, D. / Comeau, S.R. / Lindberg, A.P. / Kopacz, K.J. / Conley, G.P. / Chen, J. / Viswanathan, M. / Kastrapeli, N. / Cosic, J. / Mason, S. / DiLeo, M. ...Authors: Kenniston, J.A. / Faucette, R.R. / Martik, D. / Comeau, S.R. / Lindberg, A.P. / Kopacz, K.J. / Conley, G.P. / Chen, J. / Viswanathan, M. / Kastrapeli, N. / Cosic, J. / Mason, S. / DiLeo, M. / Abendroth, J. / Kuzmic, P. / Ladner, R.C. / Edwards, T.E. / TenHoor, C. / Adelman, B.A. / Nixon, A.E. / Sexton, D.J.
History
DepositionMar 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Sep 20, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: DX-2930 HEAVY CHAIN
L: DX-2930 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5213
Polymers47,4852
Non-polymers351
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-37 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.930, 60.540, 150.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody DX-2930 HEAVY CHAIN


Mass: 24039.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: S6C4R2*PLUS
#2: Antibody DX-2930 LIGHT CHAIN


Mass: 23446.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z3Y4*PLUS
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.5
Details: FAB DX-2930 AT 268 UM OR 12.7 MG/ML AGAINST JCSG SCREEN CONDITION H3 AND ADDITIVE SCREEN 25% PEG-3350, 0.1 M BISTRIS PH 5.5, 0.1 M SODIUM CITRATE PH 4.5, 3% V/V DMSO, SUPPLEMENTED WITH 15% ...Details: FAB DX-2930 AT 268 UM OR 12.7 MG/ML AGAINST JCSG SCREEN CONDITION H3 AND ADDITIVE SCREEN 25% PEG-3350, 0.1 M BISTRIS PH 5.5, 0.1 M SODIUM CITRATE PH 4.5, 3% V/V DMSO, SUPPLEMENTED WITH 15% V/V ETHYLENE GLYCOL AS CRYO-PROTECTANT, PUCK ID TOZ7-6, CRYSTAL TRACKING ID 243341C6, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97982 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97982 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 43347 / Num. obs: 42967 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 26.55 Å2 / Rmerge(I) obs: 0.051 / Χ2: 1.01 / Net I/σ(I): 22.43
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.78 / Num. measured obs: 2826 / Num. unique obs: 560 / % possible all: 99.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.74 Å
Translation3.5 Å19.74 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4OGX

4ogx


Resolution: 1.75→39.23 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2052 / WRfactor Rwork: 0.1654 / FOM work R set: 0.8727 / SU B: 4.575 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1155 / SU Rfree: 0.1149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2167 5.1 %RANDOM
Rwork0.172 ---
obs0.174 42901 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.67 Å2 / Biso mean: 22.06 Å2 / Biso min: 11.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å2-0 Å2-0 Å2
2---0.59 Å2-0 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 1 479 3634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023278
X-RAY DIFFRACTIONr_bond_other_d0.0010.022982
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.954489
X-RAY DIFFRACTIONr_angle_other_deg0.8223.0036877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9545439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3224.098122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61915503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2051514
X-RAY DIFFRACTIONr_chiral_restr0.10.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213767
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02739
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3511.3281711
X-RAY DIFFRACTIONr_mcbond_other1.3451.3261710
X-RAY DIFFRACTIONr_mcangle_it2.2581.9762135
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 160 -
Rwork0.242 2977 -
all-3137 -
obs--99.81 %
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)
10.65960.43880.10970.99160.28140.4733-0.02960.013-0.0768-0.02760.0504-0.0998-0.00260.0111-0.02090.09690.01610.01540.00750.00660.06417.3365.77221.063
20.58160.0811-0.05160.6457-0.0560.0356-0.050.00920.00750.03610.07580.0778-0.033-0.0154-0.02580.12510.01270.02240.0220.02340.04833.08214.05516.45
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H2 - 223
2X-RAY DIFFRACTION2L1 - 212

+
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