[English] 日本語
Yorodumi
- PDB-6p9h: Crystal structure of human anti staphylococcus aureus antibody ST... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p9h
TitleCrystal structure of human anti staphylococcus aureus antibody STAU-281 Fab in complex with IsdB NEAT2 domain
Components
  • Human anti staphylococcus aureus antibody STAU-281 Fab heavy chain
  • Human anti staphylococcus aureus antibody STAU-281 Fab light chain
  • Iron-regulated heme-iron binding protein
KeywordsIMMUNE SYSTEM / iron-regulated surface determinant system / IsdB / NEAT2 domain / antibody
Function / homology
Function and homology information


heme transmembrane transporter activity / extracellular region / metal ion binding
Similarity search - Function
Iron-regulated surface determinant protein IsdB / : / Iron-regulated surface determinant protein H/B, linker domain / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / YSIRK type signal peptide ...Iron-regulated surface determinant protein IsdB / : / Iron-regulated surface determinant protein H/B, linker domain / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Iron-regulated surface determinant protein B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 Å
AuthorsDong, J. / Crowe, J.E.
CitationJournal: Mbio / Year: 2019
Title: Human V H 1-69 Gene-Encoded Human Monoclonal Antibodies against Staphylococcus aureus IsdB Use at Least Three Distinct Modes of Binding To Inhibit Bacterial Growth and Pathogenesis.
Authors: Bennett, M.R. / Dong, J. / Bombardi, R.G. / Soto, C. / Parrington, H.M. / Nargi, R.S. / Schoeder, C.T. / Nagel, M.B. / Schey, K.L. / Meiler, J. / Skaar, E.P. / Crowe Jr., J.E.
History
DepositionJun 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 6, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Iron-regulated heme-iron binding protein
C: Human anti staphylococcus aureus antibody STAU-281 Fab heavy chain
D: Human anti staphylococcus aureus antibody STAU-281 Fab light chain
A: Iron-regulated heme-iron binding protein
H: Human anti staphylococcus aureus antibody STAU-281 Fab heavy chain
L: Human anti staphylococcus aureus antibody STAU-281 Fab light chain


Theoretical massNumber of molelcules
Total (without water)122,0196
Polymers122,0196
Non-polymers00
Water21612
1
B: Iron-regulated heme-iron binding protein
C: Human anti staphylococcus aureus antibody STAU-281 Fab heavy chain
D: Human anti staphylococcus aureus antibody STAU-281 Fab light chain


Theoretical massNumber of molelcules
Total (without water)61,0103
Polymers61,0103
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-33 kcal/mol
Surface area24170 Å2
MethodPISA
2
A: Iron-regulated heme-iron binding protein
H: Human anti staphylococcus aureus antibody STAU-281 Fab heavy chain
L: Human anti staphylococcus aureus antibody STAU-281 Fab light chain


Theoretical massNumber of molelcules
Total (without water)61,0103
Polymers61,0103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-32 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.591, 115.296, 88.273
Angle α, β, γ (deg.)90.00, 100.12, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Iron-regulated heme-iron binding protein


Mass: 13896.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: isdB, SAMEA1708674_03096 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D4RDN9, UniProt: Q2FZF0*PLUS
#2: Antibody Human anti staphylococcus aureus antibody STAU-281 Fab heavy chain


Mass: 23915.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Human anti staphylococcus aureus antibody STAU-281 Fab light chain


Mass: 23196.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate tribasic, pH 5.5, 16% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3→48.04 Å / Num. obs: 28660 / % possible obs: 99.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.2
Reflection shellResolution: 3→3.16 Å / Rmerge(I) obs: 0.316 / Num. unique obs: 4141

-
Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RTL

3rtl


Resolution: 3.003→48.039 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.19
RfactorNum. reflection% reflection
Rfree0.225 1325 4.63 %
Rwork0.2064 --
obs0.2073 28630 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.003→48.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8154 0 0 12 8166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028327
X-RAY DIFFRACTIONf_angle_d0.51911326
X-RAY DIFFRACTIONf_dihedral_angle_d10.4574959
X-RAY DIFFRACTIONf_chiral_restr0.0431286
X-RAY DIFFRACTIONf_plane_restr0.0041462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0025-3.12270.34721340.3092985X-RAY DIFFRACTION99
3.1227-3.26480.33211430.2753032X-RAY DIFFRACTION100
3.2648-3.43690.30961310.25133043X-RAY DIFFRACTION100
3.4369-3.65220.2461530.23043018X-RAY DIFFRACTION100
3.6522-3.9340.24261450.21853019X-RAY DIFFRACTION100
3.934-4.32970.20461390.18633051X-RAY DIFFRACTION100
4.3297-4.95570.1691630.16093041X-RAY DIFFRACTION100
4.9557-6.24150.20991660.18433027X-RAY DIFFRACTION100
6.2415-48.04480.19491510.1913089X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 27.5803 Å / Origin y: 9.7445 Å / Origin z: -15.1242 Å
111213212223313233
T0.3736 Å2-0.0149 Å20.0084 Å2-0.2679 Å20.0659 Å2--0.3321 Å2
L0.7362 °2-0.2199 °20.0027 °2-0.354 °20.1855 °2--0.4433 °2
S-0.0215 Å °0.0427 Å °-0.0372 Å °0.0171 Å °-0.0009 Å °0.022 Å °-0.0323 Å °0.0887 Å °0.0144 Å °
Refinement TLS groupSelection details: all

+
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://pdbjlvh1.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