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- PDB-3fnb: Crystal structure of acylaminoacyl peptidase SMU_737 from Strepto... -

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Basic information

Entry
Database: PDB / ID: 3fnb
TitleCrystal structure of acylaminoacyl peptidase SMU_737 from Streptococcus mutans UA159
ComponentsAcylaminoacyl peptidase SMU_737
KeywordsHYDROLASE / alpha-beta-alpha sandwich / helix bundle / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


serine-type endopeptidase activity
Similarity search - Function
acylaminoacyl peptidase / Serine aminopeptidase, S33 / de novo design (two linked rop proteins) / Serine aminopeptidase, S33 / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Up-down Bundle / Rossmann fold ...acylaminoacyl peptidase / Serine aminopeptidase, S33 / de novo design (two linked rop proteins) / Serine aminopeptidase, S33 / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / TRIETHYLENE GLYCOL / Hydrolase_4 domain-containing protein
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1178 Å
AuthorsKim, Y. / Hatzos, C. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of acylaminoacyl-peptidase SMU_737 from Streptococcus mutans UA159
Authors: Kim, Y. / Hatzos, C. / Cobb, G. / Joachimiak, A.
History
DepositionDec 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 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: Acylaminoacyl peptidase SMU_737
B: Acylaminoacyl peptidase SMU_737
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,08810
Polymers93,4582
Non-polymers6298
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-17.9 kcal/mol
Surface area28320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.832, 56.468, 99.901
Angle α, β, γ (deg.)90.00, 93.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acylaminoacyl peptidase SMU_737


Mass: 46729.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-term His-tag with TEV protease cut-site / Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU_737 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DUZ1

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Non-polymers , 5 types, 259 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.07 Å3/Da / Density % sol: 40.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di-Ammonium hydrogen citrate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2008 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→43.617 Å / Num. all: 40750 / Num. obs: 40750 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 9.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / Num. unique all: 1534 / % possible all: 70.7

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Processing

Software
NameClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1178→43.617 Å / SU ML: 0.28 / Cross valid method: Throught / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2060 5.08 %random
Rwork0.173 ---
all0.176 40513 --
obs0.176 40513 92.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.38 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6009 Å20 Å20.1533 Å2
2--10.8628 Å20 Å2
3----7.262 Å2
Refinement stepCycle: LAST / Resolution: 2.1178→43.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6009 0 38 251 6298
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_deg1.23
X-RAY DIFFRACTIONf_dihedral_angle_d20.73
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1178-2.16710.2908810.2333178163
2.1671-2.22130.30161060.2219205475
2.2213-2.28140.2621210.217217279
2.2814-2.34850.27521340.2159238387
2.3485-2.42430.25831470.2311254193
2.4243-2.51090.28331410.2232269197
2.5109-2.61140.2841450.2079272798
2.6114-2.73030.27861280.1984272898
2.7303-2.87420.2461520.1814274598
2.8742-3.05420.23561540.1822272899
3.0542-3.290.23411410.1795278399
3.29-3.62090.23081620.1577272999
3.6209-4.14450.19341460.1425277299
4.1445-5.22030.15561400.1325281299
5.2203-43.62620.21631620.1704280798
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)
11.6144-0.3106-0.31130.80450.60011.95660.01980.2350.2460.00780.097-0.1982-0.03350.0924-0.11620.2206-0.020.00090.2280.03220.28029.659726.195783.4774
21.88730.2189-0.85031.1843-0.05771.59940.20980.33260.2981-0.2680.03370.1438-0.1242-0.1927-0.2430.24950.04910.00780.2630.04360.2217-21.586326.206764.8861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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