[English] 日本語
Yorodumi
- PDB-3mxv: Crystal structure of fab fragment of anti-Shh 5E1 chimera -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mxv
TitleCrystal structure of fab fragment of anti-Shh 5E1 chimera
Components
  • fab fragment of anti-Shh 5E1 mouse/human chimera, heavy chain
  • fab fragment of anti-Shh 5E1 mouse/human chimera, light chain
KeywordsIMMUNE SYSTEM / chimera / fab fragment / antibody / sonic hedgehog
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHymowitz, S.G. / Maun, H.R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Hedgehog pathway antagonist 5E1 binds hedgehog at the pseudo-active site.
Authors: Maun, H.R. / Wen, X. / Lingel, A. / de Sauvage, F.J. / Lazarus, R.A. / Scales, S.J. / Hymowitz, S.G.
History
DepositionMay 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 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
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: fab fragment of anti-Shh 5E1 mouse/human chimera, light chain
H: fab fragment of anti-Shh 5E1 mouse/human chimera, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0136
Polymers47,6292
Non-polymers3844
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-72 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.287, 110.287, 122.509
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Antibody fab fragment of anti-Shh 5E1 mouse/human chimera, light chain


Mass: 23507.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli)
#2: Antibody fab fragment of anti-Shh 5E1 mouse/human chimera, heavy chain


Mass: 24121.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4
Details: protein (20 mM Hepes, pH 7.2, 0.1 M NaCl, 5 mM CaCl2) was mixed with equal volumes of reservoir solution (0.2M Ammonium Sulfate, 20% (w/v) PEG 4000), VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2008
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 43883 / Num. obs: 43883 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.07 / Net I/σ(I): 15.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 4395 / Rsym value: 0.482 / % possible all: 100

-
Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FVE

1fve


Resolution: 1.9→44.5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.376 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): -3 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22387 4370 10 %RANDOM
Rwork0.17853 ---
all0.18303 43833 --
obs0.18303 43833 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.459 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 20 352 3683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223444
X-RAY DIFFRACTIONr_angle_refined_deg1.2051.9564702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2785441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88524.748139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50515553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3971511
X-RAY DIFFRACTIONr_chiral_restr0.0770.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022592
X-RAY DIFFRACTIONr_nbd_refined0.1860.21430
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22328
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2331
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.228
X-RAY DIFFRACTIONr_mcbond_it2.3252.52216
X-RAY DIFFRACTIONr_mcangle_it3.3253527
X-RAY DIFFRACTIONr_scbond_it2.8342.51407
X-RAY DIFFRACTIONr_scangle_it4.16951169
LS refinement shellResolution: 1.9→1.939 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.297 266 -
Rwork0.218 2383 -
obs--99.92 %
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)
10.48640.2750.22811.35640.58470.80230.0120.0658-0.0751-0.08720.1016-0.2603-0.08620.194-0.1136-0.0464-0.01280.048-0.0044-0.0056-0.044533.41154.57623.6057
21.04050.13410.29290.57790.31831.1405-0.0695-0.08720.2144-0.0295-0.01890.0705-0.1794-0.07590.0884-0.04080.0221-0.0169-0.0501-0.0107-0.041818.63422.971427.9884
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 107
2X-RAY DIFFRACTION1H1 - 110
3X-RAY DIFFRACTION2L108 - 212
4X-RAY DIFFRACTION2H111 - 214

+
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