[English] 日本語
Yorodumi
- PDB-5dr5: Crystal structure of the sclerostin-neutralizing Fab AbD09097 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dr5
TitleCrystal structure of the sclerostin-neutralizing Fab AbD09097
Components
  • AbD09097 Fab heavy chain
  • AbD09097 Fab light chain
KeywordsIMMUNE SYSTEM / sclerostin-neutralizing / Fab / Wnt inhibitor
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsMueller, T.D. / Boschert, V. / Weidauer, S.E. / Muth, E.M. / Knappik, A. / Frisch, C.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationDFG MU1095/5-1 Germany
European UnionTALOS, HEALTH-F2-2008-201099
CitationJournal: to be published
Title: Generation and Affinity Maturation of Neutralizing Anti-Sclerostin Antibodies
Authors: Boschert, V. / Frisch, C. / Back, J.W. / van Pee, K. / Weidauer, S.E. / Muth, E.-M. / Schmieder, P. / Beerbaum, M. / Knappik, A. / Timmerman, P. / Mueller, T.D.
History
DepositionSep 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: AbD09097 Fab heavy chain
L: AbD09097 Fab light chain


Theoretical massNumber of molelcules
Total (without water)50,2462
Polymers50,2462
Non-polymers00
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-23 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.193, 78.495, 59.196
Angle α, β, γ (deg.)90.000, 95.710, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody AbD09097 Fab heavy chain


Mass: 26727.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The Fab heavy chain contains a C-terminal Myc- and hexahistidine extension preceded by thrombin peptidase recognition sequence to facilitate detection and purification
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1F-
#2: Antibody AbD09097 Fab light chain


Mass: 23517.982 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) / Strain (production host): TGF1-
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (w/v) PEG3350, 0.1M HEPES pH 7.5, 10mM zinc chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 13, 2012 / Details: Rigaku VariMax HF
RadiationMonochromator: multilayer mirror optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→20.77 Å / Num. all: 35146 / Num. obs: 34389 / % possible obs: 97.9 % / Redundancy: 3.66 % / Rmerge(I) obs: 0.068 / Χ2: 0.97 / Net I/σ(I): 10.5 / Num. measured all: 126958 / Scaling rejects: 953
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.85-1.922.940.33.7826128031.073280.1
1.92-1.993.490.2963.91210334431.098699
1.99-2.083.660.2494.51287734931.0478100
2.08-2.193.670.2214.91298435021.03116100
2.19-2.333.710.25.41312835111.04105100
2.33-2.513.750.147.31333435320.9474100
2.51-2.763.790.09610.11326634770.938799.9
2.76-3.163.820.06414.11351035170.868299.9
3.16-3.983.840.0518.71368635370.8789100
3.98-20.773.810.03428.11380935740.8820499.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.85 Å20.77 Å
Translation1.85 Å20.77 Å

-
Processing

Software
NameVersionClassification
CrystalClear9.2SSIdata collection
CrystalClear9.2SSIdata reduction
CrystalClear9.2SSIdata scaling
PHASER2.5.5phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3NH7

3nh7


Resolution: 1.85→20.77 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2371 / WRfactor Rwork: 0.1797 / FOM work R set: 0.7912 / SU B: 9.789 / SU ML: 0.141 / SU R Cruickshank DPI: 0.1613 / SU Rfree: 0.1552 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 1721 5 %RANDOM
Rwork0.1884 ---
obs0.1913 32559 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK / Bsol: 250.008 Å2 / ksol: 0.77 e/Å3
Displacement parametersBiso max: 71.06 Å2 / Biso mean: 29.759 Å2 / Biso min: 13.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å2-1.18 Å2
2---0.23 Å20 Å2
3----0.4 Å2
Refine analyzeLuzzati coordinate error free: 0.263 Å
Refinement stepCycle: final / Resolution: 1.85→20.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 0 288 3634
Biso mean---34.33 -
Num. residues----439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.023446
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.9544693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5635437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14524.101139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04915549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5291516
X-RAY DIFFRACTIONr_chiral_restr0.1330.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212608
X-RAY DIFFRACTIONr_mcbond_it1.72.0541754
X-RAY DIFFRACTIONr_mcangle_it2.5173.0692189
X-RAY DIFFRACTIONr_scbond_it2.2912.1891692
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 88 -
Rwork0.361 1900 -
all-1988 -
obs--76.85 %
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)
11.3525-0.60260.84662.5996-0.22061.9231-0.0144-0.0316-0.02540.1257-0.00340.15790.1488-0.19560.01780.0371-0.03260.03880.0935-0.03510.06585.2199-1.62433.0406
21.49710.77260.78571.39970.65781.5611-0.26790.07890.1955-0.24160.05160.1132-0.3491-0.10330.21630.08940.0097-0.05460.0246-0.00410.037913.466919.11320.7982
30.94360.22050.97920.9953-0.01571.59650.0474-0.1595-0.0072-0.061-0.00170.06710.0599-0.1166-0.04570.0133-0.01770.00870.09280.01090.055924.11672.664832.1163
41.093-0.48860.83621.7198-0.54411.1181-0.043-0.02220.03490.06790.0085-0.1184-0.0384-0.02620.03450.01540.00050.01420.0108-0.00050.037837.36928.326827.5698
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 115
2X-RAY DIFFRACTION2L1 - 109
3X-RAY DIFFRACTION3H116 - 224
4X-RAY DIFFRACTION4L110 - 215

+
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