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- PDB-3kds: apo-FtsH crystal structure -

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Basic information

Entry
Database: PDB / ID: 3kds
Titleapo-FtsH crystal structure
ComponentsCell division protein FtsH
KeywordsMETAL BINDING PROTEIN / Met-turn / beta roll
Function / homology
Function and homology information


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 / identical protein binding / plasma membrane
Similarity search - Function
Peptidase M41 / Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain ...Peptidase M41 / Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-NHX / ATP-dependent zinc metalloprotease FtsH
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.601 Å
AuthorsBieniossek, C. / Niederhauser, B. / Baumann, U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The crystal structure of apo-FtsH reveals domain movements necessary for substrate unfolding and translocation
Authors: Bieniossek, C. / Niederhauser, B. / Baumann, U.M.
History
DepositionOct 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Cell division protein FtsH
F: Cell division protein FtsH
G: Cell division protein FtsH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,8089
Polymers154,2423
Non-polymers1,5666
Water0
1
E: Cell division protein FtsH
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)311,61518
Polymers308,4846
Non-polymers3,13212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area22550 Å2
ΔGint-91 kcal/mol
Surface area108370 Å2
MethodPISA
2
F: Cell division protein FtsH
G: Cell division protein FtsH
hetero molecules

F: Cell division protein FtsH
G: Cell division protein FtsH
hetero molecules

F: Cell division protein FtsH
G: Cell division protein FtsH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,61518
Polymers308,4846
Non-polymers3,13212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area23140 Å2
ΔGint-82 kcal/mol
Surface area108340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.500, 190.500, 152.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Cell division protein FtsH /


Mass: 51413.938 Da / Num. of mol.: 3 / Fragment: cytosolic region, residues 146-610 / Mutation: K207A,K410L,K415A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: FtsH / Plasmid: pET-28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9WZ49
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NHX / N-{(2R)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}-3-naphthalen-2-yl-L-alanyl-L-alaninamide


Mass: 456.535 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H32N4O5

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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: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG400, 200mM CaCl2, 100mM Hepes, 200mM glycine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.987 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 1, 2006
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 50229 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 64.29 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 20.59
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.911 / Mean I/σ(I) obs: 1.9 / Num. measured obs: 15453 / Num. unique all: 3591 / Num. unique obs: 3602 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 2CE7

2ce7


Resolution: 2.601→45.757 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.77 / SU ML: 0.38 / Isotropic thermal model: Isotropic +TLS / Cross valid method: THROUGHOUT / σ(F): 1.99 / σ(I): -3 / Phase error: 29.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1986 3.96 %random
Rwork0.223 48222 --
obs0.226 50208 99.71 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.533 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 442.52 Å2 / Biso mean: 117.065 Å2 / Biso min: 24.83 Å2
Baniso -1Baniso -2Baniso -3
1-2.455 Å2-0 Å2-0 Å2
2--2.455 Å2-0 Å2
3----4.909 Å2
Refinement stepCycle: LAST / Resolution: 2.601→45.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9892 0 102 0 9994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110151
X-RAY DIFFRACTIONf_angle_d1.36113687
X-RAY DIFFRACTIONf_chiral_restr0.0751573
X-RAY DIFFRACTIONf_plane_restr0.0051798
X-RAY DIFFRACTIONf_dihedral_angle_d16.3223872
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.601-2.6660.411350.293337347298
2.666-2.7380.2891400.26433983538100
2.738-2.8190.361400.24733823522100
2.819-2.910.3281400.24233963536100
2.91-3.0140.3031400.22934123552100
3.014-3.1350.3121410.2434093550100
3.135-3.2770.3081400.23434073547100
3.277-3.450.3141420.23234323574100
3.45-3.6660.2461420.21634443586100
3.666-3.9490.2941410.234423583100
3.949-4.3460.2511440.19334753619100
4.346-4.9740.2561440.19134853629100
4.974-6.2640.2521460.22835353681100
6.264-45.7640.2851510.213668381998
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)
15.04010.3327-1.20950.4933-0.57381.5325-0.187-0.3890.19340.27460.3915-0.0027-0.77940.142-0.17540.6077-0.00320.07150.6486-0.22180.7537.295942.610553.2034
20.8561-0.27290.02232.7286-0.09194.506-0.33330.33160.0524-1.04860.65970.0767-0.246-1.7523-0.18831.22050.3543-0.2091.25490.12270.7061-12.337776.041317.0029
32.30561.49020.36521.6466-0.60990.5791-0.81230.0160.3306-1.03530.24560.2748-0.1664-0.30740.3691.56020.0646-0.39931.3298-0.60831.374621.581582.459718.1246
45.8354-1.8416-0.72541.5574-0.41781.6631-0.7791-1.4426-1.74730.52350.80070.8495-0.01980.59420.00170.62150.2490.28061.14220.13140.93812.268630.429860.6486
50.9943-0.33771.09811.30851.68063.15530.02870.4475-0.3143-0.33560.1711-0.07720.21030.2122-0.12560.76340.0581-0.13710.6122-0.19240.558710.166470.412939.4528
62.1017-2.4692-0.41583.3372-0.4611.46320.92830.0862-0.1113-1.2307-0.6343-0.27040.14170.3713-0.17390.79050.24840.0710.6698-0.21580.608943.4873101.615941.7013
70.08540.55290.62591.526-0.39960.91340.0122-0.0224-0.00960.24310.05270.0732-0.08630.1208-0.07750.341-0.0589-0.01250.4925-0.06120.365431.933630.457932.2416
84.67580.1314-0.76670.2294-0.4660.8315-0.646-0.1304-0.12360.01150.513-0.04170.54050.06140.1190.89040.0469-0.29070.6761-0.16061.00938.520572.059649.9207
90.3082-0.68980.14442.85550.39891.9049-0.2555-0.63980.01350.50730.6601-0.87330.4570.0804-0.34780.8304-0.04890.09671.2149-0.34090.936438.6264101.550549.3176
103.4489-0.22660.21121.02940.56030.49780.0791-0.11490.03740.00910.01160.045-0.18190.1567-0.07110.2828-0.0706-0.01970.2411-0.01020.20322.965621.324412.7263
112.8298-1.14010.13750.86660.74680.78940.3042-0.04590.0302-0.25170.04380.01150.4170.0645-0.28310.63390.0682-0.10990.3458-0.06790.50989.991380.108163.1999
121.5811.3839-0.03162.01220.04471.350.2190.1753-0.0820.00150.0324-0.18950.23460.5221-0.28080.40540.09340.02040.597-0.12360.548330.838103.284962.6556
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN E AND RESID 156:231E156 - 231
2X-RAY DIFFRACTION2CHAIN F AND RESID 156:307F156 - 307
3X-RAY DIFFRACTION3CHAIN G AND RESID 156:328G156 - 328
4X-RAY DIFFRACTION4CHAIN E AND RESID 232:329E232 - 329
5X-RAY DIFFRACTION5CHAIN F AND RESID 308:448F308 - 448
6X-RAY DIFFRACTION6CHAIN G AND RESID 329:448G329 - 448
7X-RAY DIFFRACTION7CHAIN E AND RESID 330:468E330 - 468
8X-RAY DIFFRACTION8CHAIN F AND RESID 449:466F449 - 466
9X-RAY DIFFRACTION9CHAIN G AND RESID 449:463G449 - 463
10X-RAY DIFFRACTION10CHAIN E AND RESID 469:603E469 - 603
11X-RAY DIFFRACTION11CHAIN F AND RESID 467:603F467 - 603
12X-RAY DIFFRACTION12CHAIN G AND RESID 464:603G464 - 603

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