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- PDB-5jyb: Crystal structure of 3 mutant of Ba3275 (S116A, E243A, H313A), th... -

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Basic information

Entry
Database: PDB / ID: 5jyb
TitleCrystal structure of 3 mutant of Ba3275 (S116A, E243A, H313A), the member of S66 family of serine peptidases
ComponentsMccC family protein
KeywordsHYDROLASE / serine peptidase / inactive enzyme / Ba3275 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


hydrolase activity / nucleotide binding
Similarity search - Function
Murein tetrapeptidase LD-carboxypeptidase, N-terminal domain / LD-carboxypeptidase A C-terminal domain-like / Peptidase family S66 / LD-carboxypeptidase A, C-terminal domain superfamily / Murein tetrapeptide carboxypeptidase, N-terminal / LD-carboxypeptidase, N-terminal / LD-carboxypeptidase, C-terminal / LD-carboxypeptidase N-terminal domain / LD-carboxypeptidase C-terminal domain / Glucose Oxidase; domain 1 ...Murein tetrapeptidase LD-carboxypeptidase, N-terminal domain / LD-carboxypeptidase A C-terminal domain-like / Peptidase family S66 / LD-carboxypeptidase A, C-terminal domain superfamily / Murein tetrapeptide carboxypeptidase, N-terminal / LD-carboxypeptidase, N-terminal / LD-carboxypeptidase, C-terminal / LD-carboxypeptidase N-terminal domain / LD-carboxypeptidase C-terminal domain / Glucose Oxidase; domain 1 / Class I glutamine amidotransferase-like / 3-Layer(bba) Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-BUTANOL / MccC family protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.647 Å
AuthorsNocek, B. / Jedrzejczak, R. / Joachimiak, A. / CSGID / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of 3 mutant of Ba3275 (S116A, E243A, H313A), the member of S66 family of serine peptidases
Authors: Nocek, B. / Jedrzejczak, R. / Joachimiak, A. / CSGID
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MccC family protein
B: MccC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,91016
Polymers78,8852
Non-polymers2,02414
Water11,998666
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.444, 71.225, 82.700
Angle α, β, γ (deg.)90.00, 109.19, 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 MccC family protein


Mass: 39442.598 Da / Num. of mol.: 2 / Mutation: S116A,E243A, H313A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 10987 / NRS 248) (bacteria)
Strain: ATCC 10987 / NRS 248 / Gene: BCE_3281 / Production host: Escherichia coli (E. coli) / References: UniProt: Q734X3

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Non-polymers , 8 types, 680 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: SO4
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-SBT / 2-BUTANOL / 2-Butanol


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: HEPES pH 7.5 0.15 M, 2-Butanol 4.000 %(v/v), PEG 20000 16.0 %(w/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 30, 2016 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.647→40 Å / Num. obs: 82827 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 11

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Processing

Software
NameVersionClassification
PHENIXdev_1888refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F1Y

5f1y


Resolution: 1.647→36.298 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1648 3839 5.18 %0.14
Rwork0.1395 ---
obs0.1408 74065 95.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.647→36.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5511 0 123 667 6301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095848
X-RAY DIFFRACTIONf_angle_d1.2237921
X-RAY DIFFRACTIONf_dihedral_angle_d15.642201
X-RAY DIFFRACTIONf_chiral_restr0.048832
X-RAY DIFFRACTIONf_plane_restr0.0061025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6469-1.66780.2059620.1981038X-RAY DIFFRACTION34
1.6678-1.68970.2094880.21111339X-RAY DIFFRACTION45
1.6897-1.71290.2371910.21181660X-RAY DIFFRACTION55
1.7129-1.73740.21671020.19971939X-RAY DIFFRACTION63
1.7374-1.76330.21341190.19352009X-RAY DIFFRACTION67
1.7633-1.79080.22511140.19712167X-RAY DIFFRACTION71
1.7908-1.82020.19991280.1892250X-RAY DIFFRACTION74
1.8202-1.85160.21081440.18092403X-RAY DIFFRACTION80
1.8516-1.88530.19441450.16882538X-RAY DIFFRACTION84
1.8853-1.92150.1971500.1652707X-RAY DIFFRACTION89
1.9215-1.96070.17551370.15542836X-RAY DIFFRACTION93
1.9607-2.00340.17921680.15262857X-RAY DIFFRACTION95
2.0034-2.050.17061570.15032922X-RAY DIFFRACTION96
2.05-2.10120.1651440.1462900X-RAY DIFFRACTION95
2.1012-2.1580.17961760.14052787X-RAY DIFFRACTION93
2.158-2.22150.16381560.13362953X-RAY DIFFRACTION98
2.2215-2.29320.15681670.12673025X-RAY DIFFRACTION98
2.2932-2.37520.16621660.12612970X-RAY DIFFRACTION98
2.3752-2.47020.14061390.12032993X-RAY DIFFRACTION98
2.4702-2.58260.15361500.12723000X-RAY DIFFRACTION98
2.5826-2.71880.14611470.12873038X-RAY DIFFRACTION98
2.7188-2.8890.18181480.13642990X-RAY DIFFRACTION98
2.889-3.1120.16611700.13252881X-RAY DIFFRACTION94
3.112-3.42490.16132030.12872981X-RAY DIFFRACTION99
3.4249-3.920.14451570.11593041X-RAY DIFFRACTION98
3.92-4.93690.12351520.11263017X-RAY DIFFRACTION98
4.9369-36.30690.16271590.16242985X-RAY DIFFRACTION94
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)
10.66970.0481-0.44150.6329-0.18211.3476-0.02240.0814-0.0064-0.05870.00410.02480.0316-0.0940.01810.081-0.0035-0.01120.0612-0.00850.0693-27.679-1.3888-6.3241
21.0541-0.30510.55440.6155-0.47011.5515-0.0566-0.04760.11960.02870.0075-0.1682-0.07950.13860.05940.0869-0.01810.01110.10240.00810.1207-10.47638.4106-4.2266
32.23730.5158-0.17520.76050.2251.7133-0.001-0.0634-0.03520.0242-0.07050.00530.17770.09290.05230.0820.0213-0.00540.07060.01850.0652-17.7282-2.794813.4238
40.56070.1031-0.12360.69280.1591.62670.0018-0.08790.00920.0196-0.0075-0.08340.06610.2764-0.00610.06110.0160.00260.11850.01110.1081-8.14190.250610.034
51.5587-0.2041-0.62340.5775-0.22361.879-0.0745-0.1622-0.0319-0.01110.0076-0.01330.15340.13270.02010.0940.0081-0.01050.0811-0.00660.0655-26.0926-1.520546.8812
60.669-0.0027-0.23390.4752-0.01221.28460.0008-0.08660.02760.0454-0.0093-0.03340.03450.07420.0070.076-0.0026-0.0030.07880.00210.0813-28.44672.158741.4184
70.5695-0.0723-0.42790.6689-0.09761.95830.00130.03080.0025-0.02080.00460.05370.0359-0.2182-0.00950.0596-0.0068-0.00870.09710.00380.0876-39.62883.08526.1987
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 149 )
2X-RAY DIFFRACTION2chain 'A' and (resid 150 through 206 )
3X-RAY DIFFRACTION3chain 'A' and (resid 207 through 263 )
4X-RAY DIFFRACTION4chain 'A' and (resid 264 through 343 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 29 )
6X-RAY DIFFRACTION6chain 'B' and (resid 30 through 231 )
7X-RAY DIFFRACTION7chain 'B' and (resid 232 through 343 )

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