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- PDB-5k99: Crystal structure of microcin immunity protein MccF from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 5k99
TitleCrystal structure of microcin immunity protein MccF from Bacillus anthracis in complex with McC
Components
  • Microcin C
  • Microcin C7 self-immunity protein mccF
KeywordsHYDROLASE/ANTIBIOTIC / MccF / McC / Immunity protein / Microcin C / S66 hydrolase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / HYDROLASE-ANTIBIOTIC complex
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 / Microcin C7 self-immunity protein mccF / Microcin immunity protein MccF
Similarity search - Component
Biological speciesBacillus anthracis str. Sterne (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNocek, B. / Kulikovsky, A. / Severinov, K. / Dubiley, S. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of microcin immunity protein MccF from Bacillus anthracis in complex with McC
Authors: Nocek, B. / Kulikovsky, A. / Severinov, K. / Dubiley, S. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Structure summary / Category: pdbx_molecule_features
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.0May 15, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.id / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_gene_src_gene / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microcin C7 self-immunity protein mccF
C: Microcin C
B: Microcin C7 self-immunity protein mccF
D: Microcin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0196
Polymers78,3254
Non-polymers6942
Water17,421967
1
A: Microcin C7 self-immunity protein mccF
C: Microcin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5103
Polymers39,1622
Non-polymers3471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Microcin C7 self-immunity protein mccF
D: Microcin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5103
Polymers39,1622
Non-polymers3471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.275, 118.275, 55.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Microcin C7 self-immunity protein mccF / Microcin immunity protein MccF


Mass: 38398.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. Sterne (bacteria)
Gene: mccF, BA_1949, BASH2_03908 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A348A2T3, UniProt: A0A6L8PEJ7*PLUS
#2: Protein/peptide Microcin C


Mass: 763.844 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 967 / 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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Succinic acid ph 7.0, 15% Peg 3350

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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: Nov 18, 2015 / 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: 1.5→28.266 Å / Num. obs: 189029 / % possible obs: 96 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 19

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4jvo

4jvo


Resolution: 1.5→28.266 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 16.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1533 9518 5.04 %0.132
Rwork0.132 ---
obs0.1331 189029 88.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→28.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5457 0 0 973 6430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115698
X-RAY DIFFRACTIONf_angle_d1.2167765
X-RAY DIFFRACTIONf_dihedral_angle_d15.0343436
X-RAY DIFFRACTIONf_chiral_restr0.066826
X-RAY DIFFRACTIONf_plane_restr0.008997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5004-1.51740.20472000.18013561X-RAY DIFFRACTION46
1.5174-1.53530.20522050.17223870X-RAY DIFFRACTION51
1.5353-1.5540.18882960.17394014X-RAY DIFFRACTION54
1.554-1.57370.21392160.17794472X-RAY DIFFRACTION58
1.5737-1.59440.20432290.17644718X-RAY DIFFRACTION61
1.5944-1.61620.20922220.17084983X-RAY DIFFRACTION65
1.6162-1.63930.18772970.17095383X-RAY DIFFRACTION70
1.6393-1.66380.20012400.16945572X-RAY DIFFRACTION73
1.6638-1.68980.18462960.17145810X-RAY DIFFRACTION75
1.6898-1.71750.19972830.16985832X-RAY DIFFRACTION77
1.7175-1.74710.17323100.16046086X-RAY DIFFRACTION78
1.7471-1.77890.18082930.16376015X-RAY DIFFRACTION79
1.7789-1.81310.17263150.15836125X-RAY DIFFRACTION80
1.8131-1.85010.18172990.15416321X-RAY DIFFRACTION82
1.8501-1.89030.18053290.15476249X-RAY DIFFRACTION82
1.8903-1.93420.1493130.15136390X-RAY DIFFRACTION83
1.9342-1.98260.17053890.14356318X-RAY DIFFRACTION83
1.9826-2.03620.17434270.13866279X-RAY DIFFRACTION84
2.0362-2.09610.14663660.1326479X-RAY DIFFRACTION85
2.0961-2.16370.13163830.12956397X-RAY DIFFRACTION84
2.1637-2.2410.14953280.12266539X-RAY DIFFRACTION85
2.241-2.33070.15923260.11646651X-RAY DIFFRACTION86
2.3307-2.43670.14863660.12396587X-RAY DIFFRACTION86
2.4367-2.56510.15133150.12826705X-RAY DIFFRACTION87
2.5651-2.72570.13653520.12426737X-RAY DIFFRACTION88
2.7257-2.9360.15593950.12776792X-RAY DIFFRACTION89
2.936-3.23110.1464810.1267061X-RAY DIFFRACTION94
3.2311-3.69770.13523930.11737288X-RAY DIFFRACTION95
3.6977-4.65540.12113480.10197371X-RAY DIFFRACTION95
4.6554-28.27060.15133060.13076906X-RAY DIFFRACTION90
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)
10.469-0.1019-0.180.20980.1230.66670.1209-0.04330.19970.0507-0.07310.093-0.13240.0253-0.05660.17360.0080.03010.1329-0.03780.1893-22.491562.170414.261
20.47140.10020.05130.62370.14470.38410.0361-0.14410.25330.0987-0.09150.2112-0.1075-0.08720.03590.16550.01240.0390.1381-0.05440.2124-30.644559.307318.2432
30.53840.14270.03040.45640.09890.34230.01810.02810.1615-0.0236-0.0180.1511-0.114-0.03-0.00030.15580.0126-0.00240.1065-0.00370.1475-24.365756.00416.5973
40.36990.05460.03590.28920.03840.36990.0706-0.11580.10940.1187-0.07470.027-0.04020.03630.00640.1818-0.01670.01360.1448-0.02790.1278-11.376758.262121.6632
50.7094-0.0478-0.16040.21940.11060.71070.0442-0.2837-0.08170.1712-0.03980.03810.02690.00680.00490.1967-0.03010.00750.1862-0.01290.1114-10.399946.955729.4484
60.4980.1240.11210.55510.20660.21660.02030.0191-00.0195-0.0037-0.0176-0.03230.0198-0.01070.11970.0018-0.00650.1073-0.00920.098-8.78643.24099.572
72.4752-1.1301-0.04191.26550.39370.77280.071-0.01190.1571-0.04710.0074-0.0383-0.15650.0582-0.01180.1681-0.01150.00340.11930.00350.1167-2.554959.924810.8236
81.070.41860.21521.08110.8621.3491-0.03930.1281-0.0796-0.03920.0654-0.0974-0.02560.05770.00340.1017-0.0010.00280.0907-0.01410.1253-19.887312.38-0.1875
90.44880.2747-0.04840.60960.04080.2675-0.01030.017-0.17510.08260.0054-0.14820.0504-0.00170.00240.1310.0022-0.00980.1073-0.01530.1591-15.51912.05695.5623
100.75390.3609-0.00330.83550.05030.3657-0.06290.0683-0.0775-0.03290.02-0.01470.0102-0.02370.04360.0981-0.00250.00470.1007-0.02770.112-22.662418.232-1.322
110.5894-0.0948-0.2870.59470.1750.9093-0.02950.089-0.0789-0.021-0.07860.14060.0121-0.16990.08670.128-0.01470.01160.1526-0.04680.1821-39.142815.5692-1.5098
120.96140.1858-0.02510.7686-0.0440.4547-0.0412-0.1882-0.15990.17390.04260.25180.011-0.2054-0.00920.1535-0.00830.05040.1723-0.03140.1762-40.1718.264912.0935
131.42010.31770.37370.42880.19010.2775-0.07490.16790.1242-0.10060.03780.0812-0.0891-0.03810.050.13280.003-0.0280.1379-0.00520.1314-26.938833.1352-6.4367
140.59650.17070.14321.04670.22560.4903-0.00740.00720.06840.0367-0.03670.1715-0.0012-0.04890.04420.11030.0073-0.00980.1177-0.02170.142-33.867635.67714.4588
150.72650.2212-0.27122.48970.45910.7476-0.01260.05490.1166-0.1199-0.05760.289-0.1003-0.14880.04960.10880.0174-0.03090.1549-0.03610.1856-40.368935.95840.3309
160.50450.0984-0.29350.56690.1510.2458-0.02510.11210.0466-0.0615-0.06360.1526-0.1671-0.03040.05260.1346-0.0025-0.01850.1746-0.03590.1586-34.841622.1639-4.7866
171.5587-0.72540.24361.3792-0.10520.22490.02410.18810.0003-0.1752-0.1190.12580.0185-0.12940.06660.1339-0.0082-0.02740.1761-0.0520.1579-37.317720.6491-12.1588
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 82 )
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 125 )
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 177 )
5X-RAY DIFFRACTION5chain 'A' and (resid 178 through 198 )
6X-RAY DIFFRACTION6chain 'A' and (resid 199 through 319 )
7X-RAY DIFFRACTION7chain 'A' and (resid 320 through 333 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 26 )
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 82 )
10X-RAY DIFFRACTION10chain 'B' and (resid 83 through 157 )
11X-RAY DIFFRACTION11chain 'B' and (resid 158 through 177 )
12X-RAY DIFFRACTION12chain 'B' and (resid 178 through 198 )
13X-RAY DIFFRACTION13chain 'B' and (resid 199 through 230 )
14X-RAY DIFFRACTION14chain 'B' and (resid 231 through 279 )
15X-RAY DIFFRACTION15chain 'B' and (resid 280 through 302 )
16X-RAY DIFFRACTION16chain 'B' and (resid 303 through 319 )
17X-RAY DIFFRACTION17chain 'B' and (resid 320 through 333 )

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