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- PDB-3h5n: Crystal structure of E. coli MccB + ATP -

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Basic information

Entry
Database: PDB / ID: 3h5n
TitleCrystal structure of E. coli MccB + ATP
ComponentsMccB protein
KeywordsTRANSFERASE / Ubiquitin-activating enzyme / microcin / protein structure / MccC7 / peptide antibiotics / N-P bond formation
Function / homology
Function and homology information


ubiquitin-like modifier activating enzyme activity / thiosulfate-cyanide sulfurtransferase activity / nucleotidyltransferase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Outer Surface Protein A; domain 3 - #70 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Outer Surface Protein A; domain 3 / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / MccB protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRegni, C.A. / Roush, R.F. / Miller, D. / Nourse, A. / Walsh, C.T. / Schulman, B.A.
CitationJournal: Embo J. / Year: 2009
Title: How the MccB bacterial ancestor of ubiquitin E1 initiates biosynthesis of the microcin C7 antibiotic.
Authors: Regni, C.A. / Roush, R.F. / Miller, D.J. / Nourse, A. / Walsh, C.T. / Schulman, B.A.
History
DepositionApr 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 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_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MccB protein
B: MccB protein
C: MccB protein
D: MccB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,12317
Polymers157,6394
Non-polymers2,48413
Water13,169731
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16670 Å2
ΔGint-82.6 kcal/mol
Surface area52580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.847, 138.239, 80.224
Angle α, β, γ (deg.)90.000, 92.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
MccB protein


Mass: 39409.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: thrombin cleavable His-tag / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BM7006 / Gene: mccB / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q47506

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Non-polymers , 5 types, 744 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / 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: 1.96 Å3/Da / Density % sol: 37.32 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24-26% Pentaerythritol ethoxylate (15/4 EO/OH, Hampton Research), 50 mM Na Hepes pH 7.5, 100 mM MgSO4, 25 mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97926 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 2, 2007 / Details: Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(220) sagital focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 96263 / Num. obs: 96263 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.054 / Χ2: 1.026 / Net I/σ(I): 19.166
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.364 / Num. unique all: 9202 / Χ2: 1.036 / % possible all: 89

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
X-GENdata scaling
HKL-2000data reduction
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H5A

3h5a


Resolution: 1.9→42.64 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.787 / SU B: 4.708 / SU ML: 0.136 / SU R Cruickshank DPI: 0.217 / SU Rfree: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 4421 5 %RANDOM
Rwork0.204 84354 --
obs0.207 88775 93.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.74 Å2 / Biso mean: 22.839 Å2 / Biso min: 8.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0.15 Å2
2---0.43 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10428 0 137 731 11296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210781
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.96214670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1551336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.70724.938480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.052151742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1831542
X-RAY DIFFRACTIONr_chiral_restr0.0910.21638
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028144
X-RAY DIFFRACTIONr_nbd_refined0.2030.25257
X-RAY DIFFRACTIONr_nbtor_refined0.3080.27416
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2877
X-RAY DIFFRACTIONr_metal_ion_refined0.0640.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.223
X-RAY DIFFRACTIONr_mcbond_it0.9091.56850
X-RAY DIFFRACTIONr_mcangle_it1.129210753
X-RAY DIFFRACTIONr_scbond_it2.02134523
X-RAY DIFFRACTIONr_scangle_it2.8524.53917
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 307 -
Rwork0.315 6058 -
all-6365 -
obs--90.12 %

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