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- PDB-3h5a: Crystal structure of E. coli MccB -

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Basic information

Entry
Database: PDB / ID: 3h5a
TitleCrystal structure of E. coli MccB
ComponentsMccB protein
KeywordsTRANSFERASE / Ubiquitin-activating enzymes / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 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 21, 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
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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)161,0568
Polymers160,7954
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17400 Å2
ΔGint-89.6 kcal/mol
Surface area61490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.649, 145.035, 158.688
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
MccB protein


Mass: 40198.637 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 5.18 Å3/Da / Density % sol: 76.24 %
Crystal growTemperature: 277.2 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.1 M NaCl, 100 mM Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.28290, 1.28330, 1.25000
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2007
RadiationMonochromator: KOHZU / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28291
21.28331
31.251
ReflectionRedundancy: 7 % / Av σ(I) over netI: 27.22 / Number: 574278 / Rmerge(I) obs: 0.101 / Χ2: 2.02 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 81993 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.035099.810.062.5026.9
4.796.0310010.082.8916.9
4.184.7910010.093.2447
3.84.1810010.1022.917.1
3.533.810010.1172.4487.1
3.323.5310010.1451.9447.1
3.153.3210010.1781.467.1
3.023.1510010.2291.1057.1
2.93.0210010.3080.8287.1
2.82.999.810.3780.7736.5
ReflectionResolution: 2.8→50 Å / Num. all: 81993 / Num. obs: 81993 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 71.2 Å2 / Rmerge(I) obs: 0.101 / Χ2: 2.024 / Net I/σ(I): 27.217
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.378 / Num. unique all: 8093 / Χ2: 0.773 / % possible all: 99.8

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.9 Å / D res low: 50 Å / FOM : 0.27 / Reflection: 73255
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
3 wavelength111.28295.06-8.33
3 wavelength121.28332.02-9.99
3 wavelength131.253.69-2.95
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Zn600.3680.6090.1440.999
2Zn48.4590.510.8940.1150.627
3Zn45.7580.6410.8830.1060.669
4Zn600.3560.7410.1350.781
Phasing MAD shell
Resolution (Å)FOM Reflection
10.46-500.533613
6.6-10.460.536146
5.16-6.60.447816
4.37-5.160.369122
3.86-4.370.2810295
3.5-3.860.2111298
3.22-3.50.1412150
3-3.220.0912815
Phasing dmFOM : 0.65 / FOM acentric: 0.64 / FOM centric: 0.67 / Reflection: 80355 / Reflection acentric: 74216 / Reflection centric: 6139
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8-49.6950.950.950.9237733003770
5-80.880.880.821112798911236
4-50.860.870.813818126701148
3.5-40.760.760.691377912845934
3-3.50.530.530.4824214228271387
2.8-30.260.260.261364412980664

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.1phasing
RESOLVE2.1phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
BOSdata collection
RefinementMethod to determine structure: MAD / Resolution: 2.8→49.69 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.232 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.813 / SU B: 10.868 / SU ML: 0.211 / SU R Cruickshank DPI: 0.366 / SU Rfree: 0.275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 4120 5 %RANDOM
Rwork0.223 77699 --
obs0.224 81819 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.13 Å2 / Biso mean: 53.742 Å2 / Biso min: 29.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å20 Å20 Å2
2---0.38 Å20 Å2
3---2.22 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11061 0 4 0 11065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02211303
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.94115351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45251414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.20624.733524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.186151840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0091547
X-RAY DIFFRACTIONr_chiral_restr0.1030.21710
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028643
X-RAY DIFFRACTIONr_nbd_refined0.2370.24834
X-RAY DIFFRACTIONr_nbtor_refined0.3190.27658
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.25
X-RAY DIFFRACTIONr_mcbond_it0.9691.57156
X-RAY DIFFRACTIONr_mcangle_it1.487211359
X-RAY DIFFRACTIONr_scbond_it2.00734595
X-RAY DIFFRACTIONr_scangle_it2.9734.53992
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 263 -
Rwork0.327 4789 -
all-5052 -
obs--83.88 %

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