[English] 日本語
Yorodumi
- PDB-2f58: IGG1 FAB FRAGMENT (58.2) COMPLEX WITH 12-RESIDUE CYCLIC PEPTIDE (... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 2f58
TitleIGG1 FAB FRAGMENT (58.2) COMPLEX WITH 12-RESIDUE CYCLIC PEPTIDE (INCLUDING RESIDUES 315-324 OF HIV-1 GP120) (MN ISOLATE)
Components
  • PROTEIN (HIV-1 GP120)
  • PROTEIN (IGG1 FAB 58.2 ANTIBODY (HEAVY CHAIN))
  • PROTEIN (IGG1 FAB 58.2 ANTIBODY (LIGHT CHAIN))
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / FAB / HIV-1 / GP120 / V3
Function / homology
Function and homology information


immunoglobulin production / adaptive immune response / immune response / extracellular space
Immunoglobulin subtype / Immunoglobulin-like domain / Immunoglobulin V-set domain / Immunoglobulin-like fold / Immunoglobulin-like domain superfamily / Immunoglobulin V-set domain / Ig-like domain profile.
Ig kappa chain V-III region PC 7183
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsStanfield, R.L. / Cabezas, E. / Satterthwait, A.C. / Stura, E.A. / Profy, A.T. / Wilson, I.A.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs.
Authors: Stanfield, R. / Cabezas, E. / Satterthwait, A. / Stura, E. / Profy, A. / Wilson, I.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 23, 1998 / Release: Feb 9, 1999
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 9, 1999Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Oct 4, 2017Structure modelRefinement descriptionsoftware_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: PROTEIN (IGG1 FAB 58.2 ANTIBODY (LIGHT CHAIN))
H: PROTEIN (IGG1 FAB 58.2 ANTIBODY (HEAVY CHAIN))
P: PROTEIN (HIV-1 GP120)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5644
Polymers49,4653
Non-polymers991
Water181
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-28 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)96.080, 114.720, 49.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein/peptide PROTEIN (IGG1 FAB 58.2 ANTIBODY (LIGHT CHAIN)) / FAB 58.2


Mass: 23573.012 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: UniProt: P01666*PLUS
#2: Protein/peptide PROTEIN (IGG1 FAB 58.2 ANTIBODY (HEAVY CHAIN)) / FAB 58.2


Mass: 24864.744 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#3: Protein/peptide PROTEIN (HIV-1 GP120) / V3 LOOP


Mass: 1027.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THIS MOLECULE WAS CHEMICALLY SYNTHESIZED
#4: Chemical ChemComp-ARN / 1-IMINO-5-PENTANONE


Mass: 99.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55 %
Crystal growpH: 5 / Details: 16% PEG4000, 0.2M IMIDAZOLE MALATE, PH 5.0

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: May 15, 1992
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→24 Å / Num. obs: 12923 / % possible obs: 91.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 35.1 Å2 / Rsym value: 0.076 / Net I/σ(I): 7.5
Reflection shellResolution: 2.8→3.02 Å / Redundancy: 1.99 % / Mean I/σ(I) obs: 1 / Rsym value: 0.288 / % possible all: 82.8

-
Processing

Software
NameVersionClassification
UCSD-systemdata collection
UCSD-systemdata reduction
MERLOTphasing
X-PLORmodel building
X-PLOR3.851refinement
UCSD-systemdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FAB 58.2 PORTION OF FAB 58.2/SER-LOOP PEPTIDE COMPLEX

Resolution: 2.8→24 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.305 615 4.8 %RANDOM
Rwork0.185 ---
Obs0.185 12923 91.9 %-
Displacement parametersBiso mean: 26.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.8→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3485 0 0 1 3486
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.8→3.02 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.366 115 5 %
Rwork0.276 2172 -
Obs--82.8 %
Xplor file

Refinement-ID: X-RAY DIFFRACTION

Serial noParam fileTopol file
1PARHCSDX.PROTOPHCSDX.PRO
2PARAM11.WATTOPH11.WAT

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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