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- PDB-3s0x: The crystal structure of GxGD membrane protease FlaK -

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Basic information

Entry
Database: PDB / ID: 3s0x
TitleThe crystal structure of GxGD membrane protease FlaK
ComponentsPeptidase A24B, FlaK domain protein
KeywordsHYDROLASE / Preflagellin Peptidase / GxGD Protease / Aspartyl Protease / intramembrane proteolysis / membrane protein
Function / homology
Function and homology information


preflagellin peptidase / membrane => GO:0016020 / aspartic-type endopeptidase activity / plasma membrane
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1220 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3240 / Prepilin type IV endopeptidase, peptidase domain / Preflagellin peptidase, C-terminal / Type IV leader peptidase family / Archaeal Peptidase A24 C-terminus Type II / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helix non-globular / Special ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1220 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3240 / Prepilin type IV endopeptidase, peptidase domain / Preflagellin peptidase, C-terminal / Type IV leader peptidase family / Archaeal Peptidase A24 C-terminus Type II / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Preflagellin peptidase
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.6 Å
AuthorsHu, J. / Xue, Y. / Ha, Y.
CitationJournal: Nature / Year: 2011
Title: The crystal structure of GXGD membrane protease FlaK.
Authors: Hu, J. / Xue, Y. / Lee, S. / Ha, Y.
History
DepositionMay 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidase A24B, FlaK domain protein
B: Peptidase A24B, FlaK domain protein


Theoretical massNumber of molelcules
Total (without water)54,1532
Polymers54,1532
Non-polymers00
Water0
1
A: Peptidase A24B, FlaK domain protein


Theoretical massNumber of molelcules
Total (without water)27,0761
Polymers27,0761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidase A24B, FlaK domain protein


Theoretical massNumber of molelcules
Total (without water)27,0761
Polymers27,0761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation2_575-x+1/2,-y+2,z+1/21
Unit cell
Length a, b, c (Å)70.895, 99.715, 118.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidase A24B, FlaK domain protein


Mass: 27076.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Gene: MmarC6_0338 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A9A677

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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: 3.87 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 9.5
Details: 30% PEG300 50 mM glycine 100 mM NaCl, pH 9.5, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.6→40 Å / Num. obs: 10106 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.6→3.73 Å / % possible all: 99.9

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Processing

Software
NameClassification
CBASSdata collection
SHELXSphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.6→38.56 Å / Cor.coef. Fo:Fc: 0.858 / Cor.coef. Fo:Fc free: 0.818 / SU B: 71.697 / SU ML: 0.504 / Cross valid method: THROUGHOUT / ESU R Free: 0.716 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.32713 1008 10.3 %RANDOM
Rwork0.26984 ---
obs0.27602 8737 96.9 %-
all-10106 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.997 Å2
Baniso -1Baniso -2Baniso -3
1-14.96 Å20 Å20 Å2
2---6.33 Å20 Å2
3----8.63 Å2
Refinement stepCycle: LAST / Resolution: 3.6→38.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 0 0 2918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223004
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.9614093
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.2625405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12222.89283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.2715417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.006155
X-RAY DIFFRACTIONr_chiral_restr0.0940.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212208
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it19.0021.52033
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it25.26223222
X-RAY DIFFRACTIONr_scbond_it33.9243971
X-RAY DIFFRACTIONr_scangle_it43.0694.5871
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 59 -
Rwork0.292 500 -
obs--92.86 %
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)
11.26360.38890.85720.49030.90963.43230.01750.0237-0.06850.0515-0.0058-0.06180.09310.0154-0.01170.1885-0.01430.0270.10150.00240.210311.030396.194342.3174
20.8356-1.22030.35828.45340.8032.20130.00240.0003-0.00220.1122-0.059-0.34320.17920.06480.05660.04350.0047-0.020.1497-0.04160.340110.40967.983725.9372
30.47840.3913-0.55490.95670.51362.8970.13390.13710.14440.10790.04490.1944-0.08080.0849-0.17870.1150.0308-0.00320.23230.03390.267715.454198.830310.8932
412.8429-9.97374.1457.8114-2.61911.90480.0123-1.4371-0.40950.06231.28730.15740.26480.583-1.29950.063-0.0606-0.12360.5584-0.08060.504533.09789.566131.3043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A498 - 623
2X-RAY DIFFRACTION1A705 - 728
3X-RAY DIFFRACTION2A624 - 704
4X-RAY DIFFRACTION3B498 - 623
5X-RAY DIFFRACTION3B705 - 728
6X-RAY DIFFRACTION4B624 - 704

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