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- PDB-5f5x: Crystal structure of S116A Ba3275 with AMP bound -

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Basic information

Entry
Database: PDB / ID: 5f5x
TitleCrystal structure of S116A Ba3275 with AMP bound
ComponentsMccC family protein Ba3275
KeywordsHYDROLASE / MccF / serine peptidase / Center for Structural Genomics of Infectious Diseases / CSGID / structural genomics
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
ADENOSINE MONOPHOSPHATE / MccC family protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.006 Å
AuthorsNocek, B. / Severinov, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of Ba3275-AMP complex from Bacillus cereus ATCC 10987
Authors: Nocek, B. / Severinov, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Structure summary
Revision 1.2Feb 8, 2017Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MccC family protein Ba3275
B: MccC family protein Ba3275
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8094
Polymers80,1152
Non-polymers6942
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MccC family protein Ba3275
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4052
Polymers40,0581
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: MccC family protein Ba3275
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4052
Polymers40,0581
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.116, 117.728, 54.852
Angle α, β, γ (deg.)90.00, 95.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MccC family protein Ba3275


Mass: 40057.504 Da / Num. of mol.: 2 / Mutation: P10A, S116A
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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q734X3
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Malate pH 5.0 0.15M, Peg 1000 %(w/v), Sodium fluoride 0.004 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 27, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→32 Å / Num. obs: 45151 / % possible obs: 97.6 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.6

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Processing

Software
NameVersionClassification
PHENIXdev_1888refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.006→31.922 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.79 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 3340 5.04 %
Rwork0.2133 --
obs0.2149 66326 92.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.006→31.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5530 0 46 278 5854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035718
X-RAY DIFFRACTIONf_angle_d0.7317752
X-RAY DIFFRACTIONf_dihedral_angle_d12.8492130
X-RAY DIFFRACTIONf_chiral_restr0.028820
X-RAY DIFFRACTIONf_plane_restr0.0031002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0059-2.03450.3399560.27361166X-RAY DIFFRACTION31
2.0345-2.06490.2555940.25741518X-RAY DIFFRACTION42
2.0649-2.09710.2954880.25491729X-RAY DIFFRACTION48
2.0971-2.13150.3031240.24611864X-RAY DIFFRACTION51
2.1315-2.16820.26531100.24351920X-RAY DIFFRACTION53
2.1682-2.20770.28971070.22232048X-RAY DIFFRACTION56
2.2077-2.25010.3011960.23362044X-RAY DIFFRACTION57
2.2501-2.2960.25161270.2282176X-RAY DIFFRACTION60
2.296-2.34590.265990.2212223X-RAY DIFFRACTION61
2.3459-2.40050.25211420.21632390X-RAY DIFFRACTION64
2.4005-2.46050.2331410.22012423X-RAY DIFFRACTION68
2.4605-2.5270.25411560.22252570X-RAY DIFFRACTION71
2.527-2.60130.23121450.2192801X-RAY DIFFRACTION76
2.6013-2.68530.23521540.21552792X-RAY DIFFRACTION79
2.6853-2.78120.23821630.22313053X-RAY DIFFRACTION83
2.7812-2.89250.2981600.22263180X-RAY DIFFRACTION86
2.8925-3.0240.25921800.22533207X-RAY DIFFRACTION89
3.024-3.18330.25281770.22383275X-RAY DIFFRACTION91
3.1833-3.38250.26191590.20933358X-RAY DIFFRACTION91
3.3825-3.64340.23191670.19843396X-RAY DIFFRACTION93
3.6434-4.00940.2121810.18743363X-RAY DIFFRACTION94
4.0094-4.58810.2191810.1853487X-RAY DIFFRACTION95
4.5881-5.77490.20351440.19943503X-RAY DIFFRACTION95
5.7749-31.9260.2911890.24143500X-RAY DIFFRACTION96
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)
11.13460.2467-0.51082.1166-0.6040.9370.0152-0.11280.02230.1386-0.03630.0986-0.03730.10180.01180.1699-0.0122-0.00430.2050.00240.17340.09525.71999.5801
21.1476-0.066-0.20670.13750.12390.81390.00740.0058-0.20840.0406-0.00830.08840.228-0.12360.0540.2829-0.04010.00640.1771-0.00260.2982-1.7431-8.6285-4.0694
32.15410.3873-0.32082.2480.11251.8799-0.0052-0.0053-0.1752-0.0907-0.0614-0.06150.03130.07420.0620.1470.00670.01890.1710.00440.185715.043-1.8284-6.4801
42.0245-0.0711-1.08022.49640.21183.7197-0.0902-0.02420.05880.10530.0445-0.00310.05890.20280.03370.17710.01-0.02420.1790.02790.160137.253423.8107-22.8585
50.84560.27430.15112.0117-0.07081.03580.02420.03220.0743-0.07860.0372-0.1447-0.05480.1052-0.02830.1565-0.0310.02710.2021-0.00630.170534.982223.0158-22.6415
61.817-1.5734-2.11792.34762.58826.2931-0.06070.2441-0.0504-0.1299-0.17330.2121-0.1575-0.38040.14190.1632-0.0551-0.01280.23870.00020.213517.187932.2343-28.5324
72.00810.1226-0.35241.9833-0.44121.538-0.0077-0.01780.02760.03710.02280.054-0.04860.035-0.01450.1915-0.00060.00940.2118-0.01670.161518.542528.0255-9.6113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 149 )
2X-RAY DIFFRACTION2chain 'A' and (resid 150 through 206 )
3X-RAY DIFFRACTION3chain 'A' and (resid 207 through 343 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 29 )
5X-RAY DIFFRACTION5chain 'B' and (resid 30 through 170 )
6X-RAY DIFFRACTION6chain 'B' and (resid 171 through 207 )
7X-RAY DIFFRACTION7chain 'B' and (resid 208 through 343 )

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