[English] 日本語
Yorodumi
- PDB-1w3z: SeMet derivative of BbCRASP-1 from Borrelia Burgdorferi -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1w3z
TitleSeMet derivative of BbCRASP-1 from Borrelia Burgdorferi
ComponentsBBCRASP-1
KeywordsCOMPLEMENT REGULATOR / COMPLEMENT REGULATOR ACQUIRING SURFACE PROTEIN / LYME BORRELIOSIS / FACTOR H BINDING / TICK / SELENOMETHIONINE
Function / homologyBbcrasp-1 / Bbcrasp-1 / Borrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / Orthogonal Bundle / Mainly Alpha / Complement regulator-acquiring surface protein 1 (CRASP-1) / Complement regulator-acquiring surface protein 1 (CRASP-1)
Function and homology information
Biological speciesBORRELIA BURGDORFERI (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsCordes, F.S. / Roversi, P. / Goodstadt, L. / Ponting, C. / Kraiczy, P. / Skerka, C. / Kirschfink, M. / Simon, M.M. / Brade, V. / Zipfel, P. ...Cordes, F.S. / Roversi, P. / Goodstadt, L. / Ponting, C. / Kraiczy, P. / Skerka, C. / Kirschfink, M. / Simon, M.M. / Brade, V. / Zipfel, P. / Wallich, R. / Lea, S.M.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2005
Title: A Novel Fold for the Factor H-Binding Protein Bbcrasp-1 of Borrelia Burgdorferi
Authors: Cordes, F.S. / Roversi, P. / Kraiczy, P. / Simon, M.M. / Brade, V. / Jahraus, O. / Wallis, R. / Skerka, C. / Zipfel, P. / Wallich, R. / Lea, S.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallisation and Preliminary Crystallographic Analysis of Bbcrasp-1, a Complement Regulator-Acquiring Surface Protein of Borrelia Burgdorferi
Authors: Cordes, F.S. / Kraiczy, P. / Roversi, P. / Kraiczy, P. / Skerka, C. / Kirschfink, M. / Simon, M.M. / Brade, V. / Lowe, E. / Zipfel, P. / Wallich, R. / Lea, S.M.
History
DepositionJul 21, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BBCRASP-1
B: BBCRASP-1


Theoretical massNumber of molelcules
Total (without water)43,1452
Polymers43,1452
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.558, 91.558, 146.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.90484, 0.41755, 0.08315), (0.42085, -0.90675, -0.02627), (0.06442, 0.05876, -0.99619)-40.57939, 154.53285, 156.76448
2given(0.91112, 0.40173, 0.09206), (0.406, -0.91328, -0.03289), (0.07087, 0.06734, -0.99521)-40.20348, 155.74326, 155.96274
3given(0.90441, 0.41835, 0.08375), (0.42224, -0.90581, -0.03497), (0.06124, 0.06699, -0.99587)-40.67791, 155.12709, 156.2002
4given(0.91442, 0.40017, 0.06075), (0.40222, -0.91518, -0.02576), (0.04529, 0.04799, -0.99782)-38.59413, 155.47997, 157.60861
5given(0.89358, 0.41709, 0.166), (0.41611, -0.90833, 0.04235), (0.16844, 0.03123, -0.98522)-47.04373, 149.63425, 157.82404

-
Components

#1: Protein BBCRASP-1


Mass: 21572.383 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 70-250
Source method: isolated from a genetically manipulated source
Details: FACTOR H BINDING DIMER SELENOMETHIONINE DERIVATIVE
Source: (gene. exp.) BORRELIA BURGDORFERI (Lyme disease spirochete)
Strain: ZS7 / Description: TICK ISOLATE GERMANY / Variant: TICK ISOLATE / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q7AUV9, UniProt: O50957*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-25 AND 251 WERE LACKING FROM THE CONSTRUCT

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 %
Description: TWO-WAVELENGTH MAD WITH PEAK AND LOW-ENERGY REMOTE LAMBDA 0.984 A
Crystal growpH: 6 / Details: 25% PEG600 200 MM IMIDAZOLE PH 6.0 5% GLYCEROL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→73.3 Å / Num. obs: 10849 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 4
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
HYSSphasing
SHARPphasing
TNT5.6refinement
RefinementMethod to determine structure: MAD / Resolution: 3.2→76.7 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT CSDX_PROTGEO / Details: BUSTER-TNT VERSION 1.0.3
RfactorNum. reflection
Rwork0.239 -
all0.24 10258
obs0.239 10824
Solvent computationSolvent model: BABINET SCALING / Bsol: 87 Å2 / ksol: 0.31 e/Å3
Refinement stepCycle: LAST / Resolution: 3.2→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 0 8 3005
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01130402
X-RAY DIFFRACTIONt_angle_deg1.01340643
X-RAY DIFFRACTIONt_dihedral_angle_d20.8218990
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0091135
X-RAY DIFFRACTIONt_gen_planes0.0154005
X-RAY DIFFRACTIONt_it2.07304020
X-RAY DIFFRACTIONt_nbd0.0631085
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

+
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://pdbjlc1.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