[English] 日本語
Yorodumi
- PDB-7zbh: ATP-dependent zinc metalloprotease FtsH (BB0789) from Borrelia bu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zbh
TitleATP-dependent zinc metalloprotease FtsH (BB0789) from Borrelia burgdorferi
ComponentsATP-dependent zinc metalloprotease FtsH
KeywordsHYDROLASE / Lyme disease / borreliosis / metalloprotease.
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / cell division / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / plasma membrane
Similarity search - Function
Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. ...Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent zinc metalloprotease FtsH
Similarity search - Component
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsBrangulis, K.
Funding support Latvia, 1items
OrganizationGrant numberCountry
Other governmentlzp-2020/2-0378 Latvia
CitationJournal: To be published
Title: ATP-dependent zinc metalloprotease FtsH (BB0789) from Borrelia burgdorferi
Authors: Brangulis, K.
History
DepositionMar 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: ATP-dependent zinc metalloprotease FtsH
B: ATP-dependent zinc metalloprotease FtsH
D: ATP-dependent zinc metalloprotease FtsH
F: ATP-dependent zinc metalloprotease FtsH
I: ATP-dependent zinc metalloprotease FtsH
K: ATP-dependent zinc metalloprotease FtsH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,47818
Polymers299,5226
Non-polymers2,95612
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23140 Å2
ΔGint-306 kcal/mol
Surface area94060 Å2
Unit cell
Length a, b, c (Å)153.810, 192.800, 114.130
Angle α, β, γ (deg.)90.000, 124.310, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22D
13A
23F
14A
24I
15A
25K
16B
26D
17B
27F
18B
28I
19B
29K
110D
210F
111D
211I
112D
212K
113F
213I
114F
214K
115I
215K

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 169 - 603 / Label seq-ID: 8 - 442

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22DC
13AA
23FD
14AA
24IE
15AA
25KF
16BB
26DC
17BB
27FD
18BB
28IE
19BB
29KF
110DC
210FD
111DC
211IE
112DC
212KF
113FD
213IE
114FD
214KF
115IE
215KF

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

-
Components

#1: Protein
ATP-dependent zinc metalloprotease FtsH


Mass: 49920.395 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: ftsH, BB_0789 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O51729, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium citrate tribasic dihydrate 0.1 M Tris pH 8.5 28% PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.3→96.75 Å / Num. obs: 40345 / % possible obs: 97.9 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Net I/σ(I): 16.3
Reflection shellResolution: 3.3→3.43 Å / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4585 / CC1/2: 0.898

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→96.75 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.809 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.73 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3316 2048 5.1 %RANDOM
Rwork0.2788 ---
obs0.2814 38297 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 314.61 Å2 / Biso mean: 118.828 Å2 / Biso min: 46.35 Å2
Baniso -1Baniso -2Baniso -3
1--3.07 Å2-0 Å2-1.45 Å2
2--4.45 Å20 Å2
3---0.31 Å2
Refinement stepCycle: final / Resolution: 3.3→96.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16228 0 0 0 16228
Num. residues----2210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01316418
X-RAY DIFFRACTIONr_bond_other_d0.0360.01615691
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.62922118
X-RAY DIFFRACTIONr_angle_other_deg2.4031.58335998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.72152163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60723.082691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.013152720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2071577
X-RAY DIFFRACTIONr_chiral_restr0.0470.22253
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218445
X-RAY DIFFRACTIONr_gen_planes_other0.0090.023334
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A110460.1
12B110460.1
21A111000.11
22D111000.11
31A110540.1
32F110540.1
41A110130.11
42I110130.11
51A110820.11
52K110820.11
61B110830.1
62D110830.1
71B111750.1
72F111750.1
81B110970.11
82I110970.11
91B112050.1
92K112050.1
101D111670.09
102F111670.09
111D110910.11
112I110910.11
121D111700.1
122K111700.1
131F111900.1
132I111900.1
141F112610.1
142K112610.1
151I112360.11
152K112360.11
LS refinement shellResolution: 3.3→3.386 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 152 -
Rwork0.359 2833 -
all-2985 -
obs--98.94 %

+
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