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- PDB-5fd8: Crystal Structure of MccF-like Protein (BA_5613) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5fd8
TitleCrystal Structure of MccF-like Protein (BA_5613) in complex with ASA (alanyl sulfamoyl adenylates)
ComponentsLD-carboxypeptidase family protein
KeywordsHYDROLASE / MccF / ASA / serine peptidase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


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
'5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE / LD-carboxypeptidase / LD-carboxypeptidase
Similarity search - Component
Biological speciesBacillus anthracis str. Ames (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsNocek, B. / Severinov, K. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of MccF-like Protein (BA_5613) in complex with ASA ( (alanyl sulfamoyl adenylates)
Authors: Nocek, B. / Severinov, K. / Joachimiak, A.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Other
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LD-carboxypeptidase family protein
B: LD-carboxypeptidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4994
Polymers74,6642
Non-polymers8352
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-6 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.777, 83.683, 130.845
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LD-carboxypeptidase family protein / Peptidase S66 / Putative carboxypeptidase yocD / Uncharacterized protein


Mass: 37332.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. Ames (bacteria)
Gene: yocD
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q81JT5, UniProt: A0A6L8PVW7*PLUS
#2: Chemical ChemComp-A5A / '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE


Mass: 417.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C13H19N7O7S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8 / Details: 30.0 % w/v PEG 3000 50 mM Bicine

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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: Jun 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: 2.05→32.31 Å / Num. obs: 37167 / % possible obs: 90 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9
Reflection shellResolution: 2.05→2.09 Å / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
PHENIXdev_1888refinement
SBC-Collectdata collection
HKL-3000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→32.309 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.85 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2004 2565 4.99 %
Rwork0.1693 --
obs0.1708 51434 90 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→32.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5145 0 56 268 5469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035339
X-RAY DIFFRACTIONf_angle_d0.7317249
X-RAY DIFFRACTIONf_dihedral_angle_d13.2031943
X-RAY DIFFRACTIONf_chiral_restr0.028832
X-RAY DIFFRACTIONf_plane_restr0.002920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0436-2.08290.2442830.21641407X-RAY DIFFRACTION34
2.0829-2.12540.2299900.21681665X-RAY DIFFRACTION40
2.1254-2.17160.2423980.20821759X-RAY DIFFRACTION42
2.1716-2.22220.2469860.2051871X-RAY DIFFRACTION45
2.2222-2.27770.25151050.2011947X-RAY DIFFRACTION47
2.2777-2.33930.24871110.18682132X-RAY DIFFRACTION51
2.3393-2.40810.23971360.18672389X-RAY DIFFRACTION58
2.4081-2.48580.22221350.19482699X-RAY DIFFRACTION65
2.4858-2.57460.24271430.19392883X-RAY DIFFRACTION69
2.5746-2.67760.20631550.18093114X-RAY DIFFRACTION74
2.6776-2.79940.22561690.19233166X-RAY DIFFRACTION76
2.7994-2.94690.24761720.19473352X-RAY DIFFRACTION80
2.9469-3.13140.19621790.18453419X-RAY DIFFRACTION82
3.1314-3.3730.20751900.16893418X-RAY DIFFRACTION82
3.373-3.7120.20291960.14963362X-RAY DIFFRACTION81
3.712-4.24810.15911750.13823455X-RAY DIFFRACTION82
4.2481-5.34820.14981620.13433455X-RAY DIFFRACTION82
5.3482-32.31350.18671800.17413376X-RAY DIFFRACTION82
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)
11.034-0.03550.45540.8817-0.37780.8398-0.00280.10570.041-0.0969-0.0106-0.09380.01260.1048-0.00330.2073-0.0030.01990.1888-0.02860.1597-0.48250.8388-50.9946
20.4925-0.07710.32140.40280.30620.5667-0.02810.04970.0626-0.04890.0552-0.0861-0.07360.1275-0.01570.1962-0.02120.0070.2043-0.00720.1931-1.19569.8565-44.0611
30.9802-0.3086-0.27411.21270.48980.7777-0.038-0.0214-0.0579-0.0573-0.00560.23220.0548-0.10310.0380.2163-0.0331-0.01070.22350.00010.2196-21.1340.9219-43.0832
40.80330.21240.46780.41340.28050.7080.0139-0.07-0.004-0.0134-0.01380.11390.0191-0.12940.00650.182-0.00510.0020.1920.00090.201-15.084613.3667-31.2545
51.1760.1073-0.25460.8439-0.07190.66880.0019-0.10770.04770.1294-0.01420.06720.0244-0.03430.01070.20390.00180.02250.2168-0.01870.1642-4.081211.5795-1.7753
61.18450.2096-0.01251.37230.38031.0435-0.0466-0.0767-0.06140.26090.0828-0.03580.01670.0033-0.01970.2744-0.01240.01030.22730.01810.19278.1633-2.5332-1.5474
71.67450.3696-0.55261.828-0.34461.23310.0372-0.0577-0.29760.1177-0.0975-0.26550.17640.13410.06740.2320.0148-0.05340.19670.01980.227412.3983-3.8152-11.5992
81.8555-0.08720.15170.9384-0.30121.0561-0.05580.1032-0.03180.14040.0464-0.229-0.11260.1406-0.010.2043-0.0038-0.01370.1816-0.00980.18424.005815.3221-19.676
90.75910.39470.5970.97020.42951.06060.0711-0.07020.02290.0957-0.11280.17130.1314-0.21490.00960.17690.0041-0.0010.2123-0.02390.21194.73992.6525-23.0702
100.92760.1542-0.08731.4027-0.65781.02-0.0778-0.04820.0269-0.26550.0432-0.13880.12370.05570.01140.1533-0.00060.03370.1833-0.0080.188810.47415.3083-22.4339
111.05020.1465-0.57520.59920.04121.82560.02750.1815-0.1082-0.1276-0.00610.04020.0929-0.0085-0.0250.19560.0081-0.01250.1676-0.00990.205613.50530.2399-20.6267
121.21880.2722-0.35760.92650.36881.92980.0718-0.1453-0.06670.0878-0.029-0.18930.05780.1094-0.06410.1757-0.02830.0080.22680.00960.22919.29927.3075-9.4096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 137 )
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 193 )
4X-RAY DIFFRACTION4chain 'A' and (resid 194 through 328 )
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 137 )
6X-RAY DIFFRACTION6chain 'B' and (resid 138 through 175 )
7X-RAY DIFFRACTION7chain 'B' and (resid 176 through 203 )
8X-RAY DIFFRACTION8chain 'B' and (resid 204 through 222 )
9X-RAY DIFFRACTION9chain 'B' and (resid 223 through 247 )
10X-RAY DIFFRACTION10chain 'B' and (resid 248 through 272 )
11X-RAY DIFFRACTION11chain 'B' and (resid 273 through 305 )
12X-RAY DIFFRACTION12chain 'B' and (resid 306 through 328 )

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