[English] 日本語
Yorodumi
- PDB-6cyf: PcrV fragment with bound Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cyf
TitlePcrV fragment with bound Fab
Components
  • IgG1 antibody, heavy chain fragment
  • IgG1 antibody, kappa light chain
  • Type III secretion system protein
KeywordsIMMUNE SYSTEM / Part of type 3 secretion system in Pseudomonas aeruginosa
Function / homology
Function and homology information


: / extracellular region
Similarity search - Function
Low calcium response V antigen / Virulence-associated V antigen superfamily / V antigen (LcrV) protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Type III secretion system protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsOganesyan, V.
CitationJournal: J. Infect. Dis. / Year: 2018
Title: Pseudomonas aeruginosa PcrV and Psl, the Molecular Targets of Bispecific Antibody MEDI3902, Are Conserved Among Diverse Global Clinical Isolates.
Authors: Tabor, D.E. / Oganesyan, V. / Keller, A.E. / Yu, L. / McLaughlin, R.E. / Song, E. / Warrener, P. / Rosenthal, K. / Esser, M. / Qi, Y. / Ruzin, A. / Stover, C.K. / DiGiandomenico, A.
History
DepositionApr 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Structure summary / Category: entity / Item: _entity.formula_weight
Revision 1.2Nov 21, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.formula_weight
Revision 1.3Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type III secretion system protein
C: IgG1 antibody, kappa light chain
D: IgG1 antibody, heavy chain fragment
B: Type III secretion system protein
L: IgG1 antibody, kappa light chain
M: IgG1 antibody, heavy chain fragment
I: Type III secretion system protein
E: IgG1 antibody, kappa light chain
F: IgG1 antibody, heavy chain fragment
Q: Type III secretion system protein
T: IgG1 antibody, kappa light chain
U: IgG1 antibody, heavy chain fragment


Theoretical massNumber of molelcules
Total (without water)246,31912
Polymers246,31912
Non-polymers00
Water1,65792
1
A: Type III secretion system protein
C: IgG1 antibody, kappa light chain
D: IgG1 antibody, heavy chain fragment


Theoretical massNumber of molelcules
Total (without water)61,5803
Polymers61,5803
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type III secretion system protein
E: IgG1 antibody, kappa light chain
F: IgG1 antibody, heavy chain fragment


Theoretical massNumber of molelcules
Total (without water)61,5803
Polymers61,5803
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
L: IgG1 antibody, kappa light chain
M: IgG1 antibody, heavy chain fragment
I: Type III secretion system protein


Theoretical massNumber of molelcules
Total (without water)61,5803
Polymers61,5803
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
Q: Type III secretion system protein
T: IgG1 antibody, kappa light chain
U: IgG1 antibody, heavy chain fragment


Theoretical massNumber of molelcules
Total (without water)61,5803
Polymers61,5803
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.686, 160.384, 260.681
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22I
13A
23Q
14C
24L
15C
25E
16C
26T
17D
27M
18D
28F
19D
29U
110B
210I
111B
211Q
112L
212E
113L
213T
114M
214F
115M
215U
116I
216Q
117E
217T
118F
218U

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNARGARGAA123 - 2472 - 126
21ASNASNARGARGBD123 - 2472 - 126
12ASNASNARGARGAA123 - 2492 - 128
22ASNASNARGARGIG123 - 2492 - 128
13ASNASNARGARGAA123 - 2472 - 126
23ASNASNARGARGQJ123 - 2472 - 126
14ALAALACYSCYSCB1 - 2141 - 214
24ALAALACYSCYSLE1 - 2141 - 214
15ALAALACYSCYSCB1 - 2141 - 214
25ALAALACYSCYSEH1 - 2141 - 214
16ALAALACYSCYSCB1 - 2141 - 214
26ALAALACYSCYSTK1 - 2141 - 214
17VALVALPROPRODC2 - 2242 - 224
27VALVALPROPROMF2 - 2242 - 224
18VALVALPROPRODC2 - 2242 - 224
28VALVALPROPROFI2 - 2242 - 224
19VALVALCYSCYSDC2 - 2272 - 227
29VALVALCYSCYSUL2 - 2272 - 227
110ASNASNARGARGBD123 - 2472 - 126
210ASNASNARGARGIG123 - 2472 - 126
111ASNASNARGARGBD123 - 2472 - 126
211ASNASNARGARGQJ123 - 2472 - 126
112ALAALACYSCYSLE1 - 2141 - 214
212ALAALACYSCYSEH1 - 2141 - 214
113ALAALACYSCYSLE1 - 2141 - 214
213ALAALACYSCYSTK1 - 2141 - 214
114GLUGLULYSLYSMF1 - 2251 - 225
214GLUGLULYSLYSFI1 - 2251 - 225
115GLUGLUPROPROMF1 - 2241 - 224
215GLUGLUPROPROUL1 - 2241 - 224
116ASNASNARGARGIG123 - 2472 - 126
216ASNASNARGARGQJ123 - 2472 - 126
117ALAALACYSCYSEH1 - 2141 - 214
217ALAALACYSCYSTK1 - 2141 - 214
118GLUGLULYSLYSFI1 - 2251 - 225
218GLUGLULYSLYSUL1 - 2251 - 225

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

-
Components

#1: Protein
Type III secretion system protein


Mass: 14027.603 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pcrV / Production host: Escherichia coli (E. coli) / References: UniProt: M4Q7H6
#2: Antibody
IgG1 antibody, kappa light chain


Mass: 23422.990 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody
IgG1 antibody, heavy chain fragment


Mass: 24129.041 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.45 Å3/Da / Density % sol: 64.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M of Ammonium Sulfate, 0.1 M of HEPES, pH 7.5 and 25% w/v of Polyethylene glycol 3350
PH range: 7-8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.775→35 Å / Num. obs: 86545 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.033 / Rrim(I) all: 0.12 / Net I/σ(I): 20.7
Reflection shellResolution: 2.775→2.784 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / Num. unique obs: 845 / CC1/2: 0.776 / Rpim(I) all: 0.547 / Rrim(I) all: 0.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JBU

4jbu


Resolution: 2.78→35 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.906 / SU B: 14.546 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.694 / ESU R Free: 0.322 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24905 4268 4.9 %RANDOM
Rwork0.2146 ---
obs0.21631 82185 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 72.479 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å2-0 Å2-0 Å2
2---2.62 Å20 Å2
3---4.98 Å2
Refinement stepCycle: 1 / Resolution: 2.78→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17164 0 0 92 17256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0217554
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215790
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.96123857
X-RAY DIFFRACTIONr_angle_other_deg0.914336858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7852239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69324.62710
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.207152841
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0531571
X-RAY DIFFRACTIONr_chiral_restr0.080.22676
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02119616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023475
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_it4.3057.2819004
X-RAY DIFFRACTIONr_mcbond_other4.2967.2819003
X-RAY DIFFRACTIONr_mcangle_it6.58610.91411227
X-RAY DIFFRACTIONr_mcangle_other6.58810.91511228
X-RAY DIFFRACTIONr_scbond_it4.1387.5218550
X-RAY DIFFRACTIONr_scbond_other4.1367.5218550
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.48611.15212631
X-RAY DIFFRACTIONr_long_range_B_refined8.82782.85618198
X-RAY DIFFRACTIONr_long_range_B_other8.82882.86618197
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A75240.06
12B75240.06
21A76560.07
22I76560.07
31A75940.07
32Q75940.07
41C127840.06
42L127840.06
51C126140.08
52E126140.08
61C126680.07
62T126680.07
71D130520.05
72M130520.05
81D130640.06
82F130640.06
91D129160.07
92U129160.07
101B75240.06
102I75240.06
111B75880.07
112Q75880.07
121L126040.07
122E126040.07
131L125260.08
132T125260.08
141M130580.07
142F130580.07
151M128660.07
152U128660.07
161I75640.07
162Q75640.07
171E125600.08
172T125600.08
181F130880.06
182U130880.06
LS refinement shellResolution: 2.775→2.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 302 -
Rwork0.38 5973 -
obs--99.98 %

+
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