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- PDB-4v0b: Escherichia coli FtsH hexameric N-domain -

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Basic information

Entry
Database: PDB / ID: 4v0b
TitleEscherichia coli FtsH hexameric N-domain
ComponentsATP-DEPENDENT ZINC METALLOPROTEASE FTSH
KeywordsHYDROLASE / MEMBRANE PROTEIN / PERIPLASMIC DOMAIN
Function / homology
Function and homology information


membrane protein complex / plasma membrane protein complex / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / plasma membrane
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 - #210 / Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / AAA ATPase, AAA+ lid domain / AAA+ lid domain ...Signal recognition particle alu RNA binding heterodimer, srp9/1 - #210 / Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent zinc metalloprotease FtsH
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSerek-Heuberger, J. / Martin, J. / Lupas, A.N. / Hartmann, M.D.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structure and Evolution of N-Domains in Aaa Metalloproteases.
Authors: Scharfenberg, F. / Serek-Heuberger, J. / Coles, M. / Hartmann, M.D. / Habeck, M. / Martin, J. / Lupas, A.N. / Alva, V.
History
DepositionSep 13, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-DEPENDENT ZINC METALLOPROTEASE FTSH
B: ATP-DEPENDENT ZINC METALLOPROTEASE FTSH
C: ATP-DEPENDENT ZINC METALLOPROTEASE FTSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7334
Polymers28,6373
Non-polymers961
Water00
1
A: ATP-DEPENDENT ZINC METALLOPROTEASE FTSH
B: ATP-DEPENDENT ZINC METALLOPROTEASE FTSH
hetero molecules

A: ATP-DEPENDENT ZINC METALLOPROTEASE FTSH
B: ATP-DEPENDENT ZINC METALLOPROTEASE FTSH
hetero molecules

A: ATP-DEPENDENT ZINC METALLOPROTEASE FTSH
B: ATP-DEPENDENT ZINC METALLOPROTEASE FTSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5629
Polymers57,2736
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area6480 Å2
ΔGint-57.7 kcal/mol
Surface area19760 Å2
MethodPISA
2
C: ATP-DEPENDENT ZINC METALLOPROTEASE FTSH
x 6


Theoretical massNumber of molelcules
Total (without water)57,2736
Polymers57,2736
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation4_575-x,-y+2,z1
crystal symmetry operation5_455y-1,-x+y,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
crystal symmetry operation6_665x-y+1,x+1,z1
Buried area6650 Å2
ΔGint-33.1 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.110, 119.110, 34.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein ATP-DEPENDENT ZINC METALLOPROTEASE FTSH / CELL DIVISION PROTEASE FTSH


Mass: 9545.575 Da / Num. of mol.: 3 / Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 25-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P0AAI3, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growDetails: 2 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.976
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.55→39 Å / Num. obs: 9209 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.12 % / Biso Wilson estimate: 58.27 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.6
Reflection shellResolution: 2.55→2.7 Å / Redundancy: 3.98 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.01 / % possible all: 86.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MUY

2muy


Resolution: 2.55→38.988 Å / SU ML: 0.32 / σ(F): 1.39 / Phase error: 30.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 643 7 %
Rwork0.2073 --
obs0.2102 9199 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→38.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1533 0 5 0 1538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031555
X-RAY DIFFRACTIONf_angle_d0.7742107
X-RAY DIFFRACTIONf_dihedral_angle_d16.154608
X-RAY DIFFRACTIONf_chiral_restr0.059246
X-RAY DIFFRACTIONf_plane_restr0.005277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.74690.31961160.30981534X-RAY DIFFRACTION89
2.7469-3.02320.3351280.24941732X-RAY DIFFRACTION100
3.0232-3.46050.29071320.21381752X-RAY DIFFRACTION100
3.4605-4.35890.24391310.19761746X-RAY DIFFRACTION100
4.3589-38.99240.21051360.1871792X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -50.5709 Å / Origin y: 59.1306 Å / Origin z: -0.3037 Å
111213212223313233
T0.4703 Å20.0498 Å2-0.08 Å2-0.3958 Å2-0.0762 Å2--0.6902 Å2
L0.249 °2-2.2613 °2-0.6184 °2-8.2787 °21.6656 °2--0.2616 °2
S-0.1265 Å °-0.107 Å °0.1566 Å °0.1615 Å °0.2401 Å °-0.7301 Å °0.174 Å °0.243 Å °-0.087 Å °
Refinement TLS groupSelection details: ALL

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