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- PDB-2di4: Crystal structure of the FtsH protease domain -

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Basic information

Entry
Database: PDB / ID: 2di4
TitleCrystal structure of the FtsH protease domain
ComponentsCell division protein ftsH homolog
KeywordsHYDROLASE / METALLOPROTEINASE / HEXAMER-RING
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 / plasma membrane
Similarity search - Function
Peptidase M41 / 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 ...Peptidase M41 / 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. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
: / ATP-dependent zinc metalloprotease FtsH
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.79 Å
AuthorsSuno, R. / Niwa, H. / Tsuchiya, D. / Zhang, X. / Yoshida, M. / Morikawa, K.
Citation
Journal: Mol.Cell / Year: 2006
Title: Structure of the Whole Cytosolic Region of ATP-Dependent Protease FtsH
Authors: Suno, R. / Niwa, H. / Tsuchiya, D. / Zhang, X. / Yoshida, M. / Morikawa, K.
#1: Journal: Structure / Year: 2002
Title: Hexameric ring structure of the ATPase domain of the membrane-integrated metalloprotease FtsH from Thermus thermophilus HB8
Authors: Niwa, H. / Tsuchiya, D. / Makyio, H. / Yoshida, M. / Morikawa, K.
History
DepositionMar 28, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein ftsH homolog
B: Cell division protein ftsH homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3334
Polymers53,9322
Non-polymers4012
Water27015
1
A: Cell division protein ftsH homolog
B: Cell division protein ftsH homolog
hetero molecules

A: Cell division protein ftsH homolog
B: Cell division protein ftsH homolog
hetero molecules

A: Cell division protein ftsH homolog
B: Cell division protein ftsH homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,00012
Polymers161,7976
Non-polymers1,2046
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area15010 Å2
ΔGint-225 kcal/mol
Surface area44850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.800, 116.800, 63.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERILEAA408 - 44112 - 45
21SERPROBB408 - 44212 - 46
32LYSARGAA458 - 52462 - 128
42HISARGBB459 - 52463 - 128
53THRLYSAA535 - 607139 - 211
63THRLYSBB535 - 607139 - 211
DetailsThe biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: -Y+1, X-Y, Z and -X+Y+1, -X+1, Z.

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Components

#1: Protein Cell division protein ftsH homolog / / Zinc protease


Mass: 26966.096 Da / Num. of mol.: 2 / Fragment: Residues 403-634
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: O67077, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES (pH 6.0), 5% PEG8K, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1.00000, 1.05000, 1.00524, 1.00714
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 4, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.051
31.005241
41.007141
ReflectionResolution: 2.79→100 Å / Num. all: 12436 / Num. obs: 12436 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Net I/σ(I): 42.9
Reflection shellResolution: 2.79→2.89 Å / Mean I/σ(I) obs: 9.9 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.79→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.889 / SU B: 28.172 / SU ML: 0.283 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.233 / ESU R Free: 0.411 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29903 876 7.1 %RANDOM
Rwork0.25092 ---
all0.2544 11487 --
obs0.2544 11487 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.51 Å2-2.25 Å20 Å2
2---4.51 Å20 Å2
3---6.76 Å2
Refinement stepCycle: LAST / Resolution: 2.79→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2628 0 2 15 2645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222667
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9733609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1075345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.48524.857105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.1415456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.21512
X-RAY DIFFRACTIONr_chiral_restr0.0860.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021956
X-RAY DIFFRACTIONr_nbd_refined0.2460.21260
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21832
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.274
X-RAY DIFFRACTIONr_metal_ion_refined0.2990.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3490.24
X-RAY DIFFRACTIONr_mcbond_it0.7421.51783
X-RAY DIFFRACTIONr_mcangle_it1.152756
X-RAY DIFFRACTIONr_scbond_it2.0253993
X-RAY DIFFRACTIONr_scangle_it2.944.5853
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1221 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.395
loose thermal1.3710
LS refinement shellResolution: 2.79→2.861 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 60 -
Rwork0.302 787 -
obs--95.92 %
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)
14.142-0.8146-0.58051.54270.13320.76890.02580.1163-0.2674-0.0542-0.0606-0.1450.1166-0.03420.03480.00250.019-0.0169-0.0901-0.0132-0.155371.42772.99537.8189
21.0815-0.5168-0.37845.07150.47550.7597-0.02560.0019-0.1896-0.0694-0.00330.220.0604-0.07660.029-0.0495-0.0347-0.0184-0.03970.0072-0.201938.37216.8837.5309
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA408 - 44112 - 45
2X-RAY DIFFRACTION1AA458 - 52462 - 128
3X-RAY DIFFRACTION1AA535 - 607139 - 211
4X-RAY DIFFRACTION2BB408 - 44212 - 46
5X-RAY DIFFRACTION2BB459 - 52463 - 128
6X-RAY DIFFRACTION2BB535 - 607139 - 211

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