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- PDB-6bxg: 1.45 Angstrom Resolution Crystal Structure of PDZ domain of Carbo... -

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Basic information

Entry
Database: PDB / ID: 6bxg
Title1.45 Angstrom Resolution Crystal Structure of PDZ domain of Carboxy-Terminal Protease from Vibrio cholerae in Complex with Peptide.
Components
  • LEU-ILE-ALA
  • Tail-specific protease
KeywordsHYDROLASE/PEPTIDE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / PDZ domain / HYDROLASE / HYDROLASE-PEPTIDE complex
Function / homology
Function and homology information


serine-type peptidase activity / peptidase activity / outer membrane-bounded periplasmic space / endopeptidase activity / signal transduction / proteolysis
Similarity search - Function
B melanoma antigen-like / B melanoma antigen family / Tail specific protease, C-terminal / C-terminal domain of tail specific protease (DUF3340) / Tail specific protease, N-terminal domain / Tail specific protease N-terminal domain / C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 ...B melanoma antigen-like / B melanoma antigen family / Tail specific protease, C-terminal / C-terminal domain of tail specific protease (DUF3340) / Tail specific protease, N-terminal domain / Tail specific protease N-terminal domain / C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 / ClpP/crotonase-like domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
IODIDE ION / Tail-specific protease
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsMinasov, G. / Shuvalova, L. / Filippova, E.V. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.45 Angstrom Resolution Crystal Structure of PDZ domain of Carboxy-Terminal Protease from Vibrio cholerae in Complex with Peptide.
Authors: Minasov, G. / Shuvalova, L. / Filippova, E.V. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tail-specific protease
B: LEU-ILE-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,51714
Polymers11,1772
Non-polymers1,34012
Water1,51384
1
A: Tail-specific protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,20113
Polymers10,8611
Non-polymers1,34012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LEU-ILE-ALA


  • defined by author
  • 315 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)3151
Polymers3151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.579, 35.579, 118.394
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Tail-specific protease


Mass: 10861.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_1496 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q9KRY7
#2: Protein/peptide LEU-ILE-ALA


Mass: 315.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: peptide belongs to not identified protein from E. coli.
Source: (natural) Escherichia coli (E. coli)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.85 Å3/Da / Density % sol: 33.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 9.7 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen: PACT (E3) 0.2M Sodium iodide, 20% (w/v) PEG 3350..

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2017 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 15127 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.021 / Rrim(I) all: 0.058 / Rsym value: 0.054 / Χ2: 1.715 / Net I/σ(I): 51.2
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 775 / CC1/2: 0.893 / Rpim(I) all: 0.3 / Rrim(I) all: 0.817 / Rsym value: 0.759 / Χ2: 1.003 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→29.82 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.1 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.066 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17758 708 4.7 %RANDOM
Rwork0.1324 ---
obs0.1346 14288 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.45→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms754 0 12 84 850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.019797
X-RAY DIFFRACTIONr_bond_other_d0.0010.02824
X-RAY DIFFRACTIONr_angle_refined_deg1.4142.021081
X-RAY DIFFRACTIONr_angle_other_deg0.80631909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3255107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.5925.35728
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.64715149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.569155
X-RAY DIFFRACTIONr_chiral_restr0.080.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.02889
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02136
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_it1.6121.604422
X-RAY DIFFRACTIONr_mcbond_other1.612421
X-RAY DIFFRACTIONr_mcangle_it2.052.419531
X-RAY DIFFRACTIONr_mcangle_other2.04933.416532
X-RAY DIFFRACTIONr_scbond_it2.071.98375
X-RAY DIFFRACTIONr_scbond_other2.071375
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5952.831550
X-RAY DIFFRACTIONr_long_range_B_refined3.902815
X-RAY DIFFRACTIONr_long_range_B_other3.779802
X-RAY DIFFRACTIONr_rigid_bond_restr11.9973797
X-RAY DIFFRACTIONr_sphericity_free28.8457
X-RAY DIFFRACTIONr_sphericity_bonded16.5154828
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 57 -
Rwork0.216 1063 -
obs--99.91 %
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)
11.5772-0.4036-0.40623.8919-0.40491.6054-0.0490.0320.03020.00220.12470.0456-0.067-0.1012-0.07570.01240.00680.00260.05450.00540.0039-12.312717.66417.2874
21.1880.37310.16651.6022-0.62551.4383-0.09320.0042-0.08480.03480.0806-0.0113-0.08450.0480.01260.03970.00320.00480.09150.00210.0095-5.022719.47493.0922
32.7656-1.6944-0.42964.0478-0.42241.7999-0.10040.0988-0.1105-0.050.14210.17480.0427-0.1945-0.04160.0254-0.0273-0.00090.0912-0.00130.0105-13.251315.8866-3.887
41.51081.1302-0.14326.4834-1.24541.3022-0.03550.0020.01070.1330.011-0.0843-0.05830.03260.02440.0146-0.0112-0.00170.0581-0.00550.0022-3.124621.9879-0.509
54.70510.0676-6.34570.0044-0.08948.5594-0.0744-0.1198-0.07070.0029-0.0089-0.01920.0940.15510.08340.08740.017-0.00380.12780.01210.1034-11.84694.320410.1283
610.0922-7.3107-3.02527.88571.62991.09710.06390.1205-0.0561-0.0001-0.05620.1096-0.0151-0.0416-0.00770.0270.00090.00230.0457-0.00130.0351-16.987214.98416.5487
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A244 - 272
2X-RAY DIFFRACTION2A273 - 289
3X-RAY DIFFRACTION3A290 - 314
4X-RAY DIFFRACTION4A315 - 336
5X-RAY DIFFRACTION5A337 - 341
6X-RAY DIFFRACTION6B1 - 3

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