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- PDB-3ih6: Crystal structure of putative zinc protease from Bordetella pertu... -

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Basic information

Entry
Database: PDB / ID: 3ih6
TitleCrystal structure of putative zinc protease from Bordetella pertussis Tohama I
ComponentsPutative zinc protease
KeywordsHYDROLASE / putative zinc protease / Bordetella pertussis Tohama I / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Protease
Function / homology
Function and homology information


metalloendopeptidase activity / metal ion binding
Similarity search - Function
Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Putative zinc protease
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsChang, C. / Chhor, G. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of putative zinc protease from Bordetella pertussis Tohama I
Authors: Chang, C. / Chhor, G. / Bearden, J. / Joachimiak, A.
History
DepositionJul 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative zinc protease
B: Putative zinc protease
C: Putative zinc protease
D: Putative zinc protease
E: Putative zinc protease
F: Putative zinc protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,94310
Polymers130,6976
Non-polymers2454
Water12,629701
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12990 Å2
ΔGint-107 kcal/mol
Surface area43610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.931, 130.977, 76.682
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Putative zinc protease


Mass: 21782.908 Da / Num. of mol.: 6 / Fragment: sequence database residues 258-451
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: BP2497 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q7VVY4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 701 / 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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M potassium Sodium Tartrate, 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 12, 2009
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 61718 / Num. obs: 59966 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 43.6
Reflection shellResolution: 2.15→2.17 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 9.08 / % possible all: 91.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→31.54 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.888 / SU B: 13.15 / SU ML: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2683 3044 5.1 %RANDOM
Rwork0.20712 ---
obs0.21024 56899 97.14 %-
all-59943 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.211 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.91 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.15→31.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8244 0 16 701 8961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228457
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.9711519
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16651077
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.43823.24358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.723151290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3581567
X-RAY DIFFRACTIONr_chiral_restr0.0950.21311
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216477
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_it0.6371.55427
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12128646
X-RAY DIFFRACTIONr_scbond_it2.10633030
X-RAY DIFFRACTIONr_scangle_it3.2514.52873
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.203 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 207 -
Rwork0.207 3867 -
obs--90.43 %
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)
11.7737-0.2708-0.6611.80940.09441.2706-0.10940.09380.0332-0.02630.0811-0.13590.1276-0.08430.02820.0445-0.00890.01880.0133-0.00310.031646.481943.310532.8861
20.6001-0.20790.8610.6389-1.20394.88160.0922-0.04820.08750.1554-0.0152-0.05920.0330.0789-0.0770.1079-0.006-0.03510.011-0.01850.072241.828152.526250.5699
32.04680.6001-0.22971.9896-0.52652.16650.0329-0.16510.3899-0.0334-0.09710.1646-0.12120.10550.06420.0516-0.0226-0.02420.0884-0.01780.09447.218750.055874.0978
42.2683-0.2409-0.57982.5381.81022.6488-0.1046-0.2011-0.12790.07490.037-0.04310.21520.03660.06770.0642-0.006-0.00670.07640.03250.027243.339229.831573
52.3612-0.34770.17990.967-0.23324.6546-0.1454-0.4674-0.48290.0710.1031-0.10710.15410.27520.04230.01890.04310.02780.1160.09450.210148.725311.343759.5107
61.09760.88460.03113.9303-0.43170.6224-0.02260.1497-0.24680.00140.04840.0374-0.0483-0.1921-0.02580.08520.0260.04540.1075-0.02160.133344.301521.609942.2238
71.68250.0377-0.21282.31640.46441.49710.0097-0.00660.13890.0752-0.02250.1353-0.0557-0.05180.01270.00820.00440.00730.00610.00680.060315.28453.907144.2995
80.86270.6026-0.20124.7364-2.00231.4755-0.02590.122-0.07550.0422-0.0088-0.05470.02240.01660.03470.0513-0.00150.00030.0195-0.01070.007220.060435.184237.4824
91.82720.05570.33871.8331-0.22841.0103-0.00990.1246-0.0738-0.17580.00070.0091-0.02080.01130.00930.0336-0.0044-0.00680.0115-0.00960.030117.730412.340144.1346
101.4191-0.3925-0.73053.26451.33791.6570.0786-0.1189-0.09060.12830.0248-0.07060.05910.0641-0.10330.0529-0.03-0.00810.040.00370.025421.845717.123263.8065
111.55480.5143-0.52792.1213-0.23770.7829-0.0779-0.2424-0.10160.08480.0905-0.02490.0680.0528-0.01250.0635-0.00560.0180.1209-0.00590.020217.166134.109279.8715
121.3602-0.52061.23990.6018-0.0055.11230.0033-0.09530.23980.0548-0.0073-0.04020.0701-0.03160.00410.0876-0.0121-0.00290.015-0.030.072220.092149.334267.0451
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A255 - 369
2X-RAY DIFFRACTION1A429 - 447
3X-RAY DIFFRACTION2A370 - 428
4X-RAY DIFFRACTION3B255 - 369
5X-RAY DIFFRACTION3B429 - 447
6X-RAY DIFFRACTION4B370 - 428
7X-RAY DIFFRACTION5C255 - 369
8X-RAY DIFFRACTION5C429 - 447
9X-RAY DIFFRACTION6C370 - 428
10X-RAY DIFFRACTION7D255 - 369
11X-RAY DIFFRACTION7D429 - 447
12X-RAY DIFFRACTION8D370 - 428
13X-RAY DIFFRACTION9E255 - 369
14X-RAY DIFFRACTION9E429 - 447
15X-RAY DIFFRACTION10E370 - 428
16X-RAY DIFFRACTION11F255 - 369
17X-RAY DIFFRACTION11F429 - 447
18X-RAY DIFFRACTION12F370 - 428

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