[English] 日本語
Yorodumi
- PDB-2f6a: Collagen Adhesin and Collagen Complex Structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2f6a
TitleCollagen Adhesin and Collagen Complex Structure
Components
  • Collagen
  • Collagen adhesin
KeywordsCELL ADHESION/STRUCTURAL PROTEIN / CNA / Collagen / MSCRAMM / Adhesion / ECM / CELL ADHESION-STRUCTURAL PROTEIN COMPLEX
Function / homology
Function and homology information


collagen binding / peptidoglycan-based cell wall / membrane => GO:0016020 / cell adhesion / extracellular region
Similarity search - Function
Collagen binding domain / Collagen binding domain / Saimiri transformation-associated protein / Collagen-binding surface protein Cna-like, B-type domain / Cna protein B-type domain / Immunoglobulin-like - #740 / Immunoglobulin-like - #1280 / Fibrogen-binding domain 1 / Prealbumin-like fold domain / Prealbumin-like fold domain ...Collagen binding domain / Collagen binding domain / Saimiri transformation-associated protein / Collagen-binding surface protein Cna-like, B-type domain / Cna protein B-type domain / Immunoglobulin-like - #740 / Immunoglobulin-like - #1280 / Fibrogen-binding domain 1 / Prealbumin-like fold domain / Prealbumin-like fold domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Adhesion domain superfamily / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Collagen adhesin / Saimiri transformation-associated protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsZong, Y. / Narayana, S.L.V.
CitationJournal: Embo J. / Year: 2005
Title: A 'Collagen Hug' model for Staphylococcus aureus CNA binding to collagen.
Authors: Zong, Y. / Xu, Y. / Liang, X. / Keene, D.R. / Hook, A. / Gurusiddappa, S. / Hook, M. / Narayana, S.V.
History
DepositionNov 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Apr 3, 2024Group: 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_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Collagen adhesin
B: Collagen adhesin
C: Collagen adhesin
D: Collagen adhesin
E: Collagen
F: Collagen
G: Collagen
H: Collagen
I: Collagen
J: Collagen


Theoretical massNumber of molelcules
Total (without water)149,22310
Polymers149,22310
Non-polymers00
Water00
1
A: Collagen adhesin
C: Collagen adhesin
E: Collagen
F: Collagen
G: Collagen


Theoretical massNumber of molelcules
Total (without water)74,6125
Polymers74,6125
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9150 Å2
ΔGint-46 kcal/mol
Surface area31540 Å2
MethodPISA
2
B: Collagen adhesin
D: Collagen adhesin
H: Collagen
I: Collagen
J: Collagen


Theoretical massNumber of molelcules
Total (without water)74,6125
Polymers74,6125
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Collagen adhesin
B: Collagen adhesin
C: Collagen adhesin
D: Collagen adhesin
E: Collagen
F: Collagen
G: Collagen
H: Collagen
I: Collagen
J: Collagen

A: Collagen adhesin
B: Collagen adhesin
C: Collagen adhesin
D: Collagen adhesin
E: Collagen
F: Collagen
G: Collagen
H: Collagen
I: Collagen
J: Collagen


Theoretical massNumber of molelcules
Total (without water)298,44620
Polymers298,44620
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area48120 Å2
ΔGint-224 kcal/mol
Surface area114370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.547, 193.820, 205.189
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13E
23F
33G
43H
53I
63J

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERVALVAL5AA35 - 1608 - 133
21SERSERVALVAL5BB35 - 1608 - 133
31SERSERVALVAL5CC35 - 1608 - 133
41SERSERVALVAL5DD35 - 1608 - 133
12TYRTYRTHRTHR4AA175 - 328148 - 301
22TYRTYRTHRTHR4BB175 - 328148 - 301
32TYRTYRTHRTHR4CC175 - 328148 - 301
42TYRTYRTHRTHR4DD175 - 328148 - 301
13GLYGLYGLYGLY6EE1 - 281 - 28
23GLYGLYGLYGLY6FF1 - 281 - 28
33GLYGLYGLYGLY6GG1 - 281 - 28
43GLYGLYGLYGLY6HH1 - 281 - 28
53GLYGLYGLYGLY6II1 - 281 - 28
63GLYGLYGLYGLY6JJ1 - 281 - 28

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein
Collagen adhesin


Mass: 33131.336 Da / Num. of mol.: 4 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cna / Production host: Escherichia coli (E. coli) / References: UniProt: Q53654
#2: Protein/peptide
Collagen


Mass: 2782.975 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Chemically synthesized collagen like peptide / References: UniProt: Q805R9*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.35
Details: 0.8 M ammonium sulfate, 0.5 M sodium acetate, PH 6.5, pH 7.35, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 12, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.29→50 Å / Num. all: 26299 / Num. obs: 24902 / % possible obs: 94.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.29→3.42 Å / % possible all: 83.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CNA

Resolution: 3.29→50 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.855 / SU B: 29.623 / SU ML: 0.471 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.68 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30795 1348 5.1 %RANDOM
Rwork0.25193 ---
all0.277 26299 --
obs0.25479 24902 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 63.632 Å2
Baniso -1Baniso -2Baniso -3
1-11.72 Å20 Å20 Å2
2---7.47 Å20 Å2
3----4.25 Å2
Refinement stepCycle: LAST / Resolution: 3.29→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10394 0 0 0 10394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0590.02210647
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg4.8441.9914539
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.68951368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.69826.216444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.51151667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2621524
X-RAY DIFFRACTIONr_chiral_restr0.4160.21634
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.028212
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3630.26090
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3770.27116
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2520.2476
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3360.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.3051.57145
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it13.061211184
X-RAY DIFFRACTIONr_scbond_it6.74833884
X-RAY DIFFRACTIONr_scangle_it9.8914.53355
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A504medium positional0.380.5
12B504medium positional0.510.5
13C504medium positional0.440.5
14D504medium positional0.450.5
21A1224medium positional0.610.5
22B1224medium positional0.820.5
23C1224medium positional0.680.5
24D1224medium positional0.860.5
11A428loose positional0.775
12B428loose positional0.815
13C428loose positional0.75
14D428loose positional0.815
31E181loose positional1.55
32F181loose positional1.235
33G181loose positional1.485
34H181loose positional1.285
35I181loose positional1.235
36J181loose positional1.85
11A504medium thermal10.312
12B504medium thermal9.592
13C504medium thermal5.082
14D504medium thermal7.132
21A1224medium thermal8.72
22B1224medium thermal8.992
23C1224medium thermal8.832
24D1224medium thermal8.142
11A428loose thermal16.1310
12B428loose thermal14.9210
13C428loose thermal13.2310
14D428loose thermal15.0310
31E181loose thermal12.5110
32F181loose thermal1310
33G181loose thermal14.4910
34H181loose thermal20.3610
35I181loose thermal12.210
36J181loose thermal20.6410
LS refinement shellResolution: 3.293→3.379 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 99 -
Rwork0.332 1583 -
obs--83.23 %

+
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