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- PDB-3gwb: Crystal structure of peptidase M16 inactive domain from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 3gwb
TitleCrystal structure of peptidase M16 inactive domain from Pseudomonas fluorescens. Northeast Structural Genomics target PlR293L
ComponentsPeptidase M16 inactive domain family protein
KeywordsHYDROLASE / peptidase M16 family / PFL_5859 / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / hydrolase activity / metal ion binding
Similarity search - Function
Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Metalloenzyme, LuxS/M16 peptidase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidase, M16 family
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsSeetharaman, J. / Chen, Y. / Fang, F. / Xiao, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of peptidase M16 inactive domain from Pseudomonas fluorescens. Northeast Structural Genomics target PlR293L
Authors: Seetharaman, J. / Chen, Y. / Fang, F. / Xiao, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMar 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase M16 inactive domain family protein
B: Peptidase M16 inactive domain family protein


Theoretical massNumber of molelcules
Total (without water)94,1782
Polymers94,1782
Non-polymers00
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-10.7 kcal/mol
Surface area34140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.673, 64.841, 114.972
Angle α, β, γ (deg.)90.00, 96.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peptidase M16 inactive domain family protein


Mass: 47089.242 Da / Num. of mol.: 2 / Fragment: UNP residues 53-479
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf-5 / Gene: PFL_5859 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4K4B6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 7
Details: 0.1 M KH2PO4, 0.1 M Tris-HCl pH 4.0, 40% PEG 4000, MICROBATCH UNDER OIL, temperature 277.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A10.979
SYNCHROTRONNSLS X4C20.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMar 14, 2009
MAR CCD 165 mm2CCDMar 20, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 118245 / Num. obs: 118245 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 7.1 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.068 / Net I/σ(I): 11
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.28 / Rsym value: 0.33 / % possible all: 83

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXDphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 266057.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: 1. The Friedel pairs were used in phasing. 2. BULK SOLVENT MODEL USED in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 5077 3.8 %RANDOM
Rwork0.2037 ---
obs0.2037 104854 77.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.7346 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.094 Å20 Å2-1.75 Å2
2--0.282 Å20 Å2
3----0.376 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6152 0 0 484 6636
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006235
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.34245
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 807 5.1 %
Rwork0.262 14966 -
obs--81.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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