[English] 日本語
Yorodumi
- PDB-4bf3: ErpC, a member of the complement regulator acquiring family of su... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bf3
TitleErpC, a member of the complement regulator acquiring family of surface proteins from Borrelia burgdorfei, possesses an architecture previously unseen in this protein family.
ComponentsERPC
KeywordsSTRUCTURAL PROTEIN / CRASP4 / CRASP-4 / BBCRASP4 / BBCRASP-4 / COMPLEMENT / FACTOR H
Function / homology
Function and homology information


Borrelia outer surface protein E/F / OspE-like superfamily / Borrelia outer surface protein E / Borrelia outer surface protein E/F / Transcriptional Co-activator pc4; Chain A / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesBORRELIA BURGDORFERI (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.37 Å
AuthorsCaesar, J.J.E. / Johnson, S. / Kraiczy, P. / Lea, S.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Erpc, a Member of the Complement Regulator-Acquiring Family of Surface Proteins from Borrelia Burgdorferi, Possesses an Architecture Previously Unseen in This Protein Family.
Authors: Caesar, J.J.E. / Johnson, S. / Kraiczy, P. / Lea, S.M.
History
DepositionMar 14, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ERPC
B: ERPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0837
Polymers36,7722
Non-polymers3105
Water43224
1
A: ERPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4482
Polymers18,3861
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ERPC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6355
Polymers18,3861
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.520, 68.160, 76.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.016, -1, 0.015), (1, -0.016, -0.019), (0.019, 0.015, 1)
Vector: -16.149, 16.157, 19.403)

-
Components

#1: Protein ERPC


Mass: 18386.232 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BORRELIA BURGDORFERI (Lyme disease spirochete)
Strain: B31-M1 / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): B834 / References: UniProt: Q44790
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN-TERMINUS CONTAINS REMAINS OF 3C PROTEASE SITE USED FOR REMOVAL OF GST TAG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.5 % / Description: NONE
Crystal growDetails: 27% (W/V) PEG 2000 MME, 0.1M SODIUM CACODYLATE PH 6.5

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2011 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.37→24.15 Å / Num. obs: 13663 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 60.43 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.7
Reflection shellResolution: 2.37→2.46 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.37→24.15 Å / Cor.coef. Fo:Fc: 0.9423 / Cor.coef. Fo:Fc free: 0.9315 / SU R Cruickshank DPI: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.292 / SU Rfree Blow DPI: 0.214 / SU Rfree Cruickshank DPI: 0.217
RfactorNum. reflection% reflectionSelection details
Rfree0.2302 675 4.95 %RANDOM
Rwork0.1899 ---
obs0.1917 13623 99.37 %-
Displacement parametersBiso mean: 56.18 Å2
Baniso -1Baniso -2Baniso -3
1-2.5211 Å20 Å20 Å2
2---8.4532 Å20 Å2
3---5.9321 Å2
Refine analyzeLuzzati coordinate error obs: 0.319 Å
Refinement stepCycle: LAST / Resolution: 2.37→24.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 20 24 2143
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012140HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.182853HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d786SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes287HARMONIC5
X-RAY DIFFRACTIONt_it2140HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.51
X-RAY DIFFRACTIONt_other_torsion19.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion281SEMIHARMONIC5
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_contact2227SEMIHARMONIC4
LS refinement shellResolution: 2.37→2.56 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2155 160 5.9 %
Rwork0.2079 2552 -
all0.2084 2712 -
obs--99.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.7317-0.23881.10312.6261-0.01253.11740.22540.2322-0.2856-0.03060.0388-0.09250.26910.2056-0.2641-0.10680.0342-0.0372-0.1146-0.0361-0.1486-10.3383-17.829128.9522
22.80660.42610.05883.20081.03283.51330.07180.09380.1773-0.17860.1293-0.2864-0.17080.2437-0.2011-0.11020.0160.0439-0.1437-0.0188-0.09892.43285.143447.8828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

+
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://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