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- PDB-4mqd: Crystal structure of ComJ, inhibitor of the DNA degrading activit... -

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Basic information

Entry
Database: PDB / ID: 4mqd
TitleCrystal structure of ComJ, inhibitor of the DNA degrading activity of NucA, from Bacillus subtilis
ComponentsDNA-entry nuclease inhibitor
KeywordsHydrolase Inhibitor / inhibitor of NucA / Competence protein J / Midwest center for structural genomics / MCSG / PSI-BIOLOGY
Function / homology
Function and homology information


establishment of competence for transformation / plasma membrane
Similarity search - Function
Competence, DNA-entry nuclease inhibitor, ComJ / Competence, DNA-entry nuclease inhibitor, ComJ / DNA-entry nuclease inhibitor, ComJ superfamily / Competence protein J (ComJ) / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA-entry nuclease inhibitor
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.16 Å
AuthorsChang, C. / Mack, J. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of ComJ, inhibitor of the DNA degrading activity of NucA, from Bacillus subtilis
Authors: Chang, C. / Mack, J. / Clancy, S. / Joachimiak, A.
History
DepositionSep 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-entry nuclease inhibitor
B: DNA-entry nuclease inhibitor
C: DNA-entry nuclease inhibitor
D: DNA-entry nuclease inhibitor


Theoretical massNumber of molelcules
Total (without water)61,8914
Polymers61,8914
Non-polymers00
Water4,846269
1
A: DNA-entry nuclease inhibitor
B: DNA-entry nuclease inhibitor


Theoretical massNumber of molelcules
Total (without water)30,9452
Polymers30,9452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA-entry nuclease inhibitor
D: DNA-entry nuclease inhibitor


Theoretical massNumber of molelcules
Total (without water)30,9452
Polymers30,9452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: DNA-entry nuclease inhibitor

B: DNA-entry nuclease inhibitor


Theoretical massNumber of molelcules
Total (without water)30,9452
Polymers30,9452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z+1/31
Buried area1300 Å2
ΔGint-10 kcal/mol
Surface area13370 Å2
MethodPISA
4
C: DNA-entry nuclease inhibitor

D: DNA-entry nuclease inhibitor


Theoretical massNumber of molelcules
Total (without water)30,9452
Polymers30,9452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_675-x+y+1,-x+2,z+1/31
Buried area1320 Å2
ΔGint-9 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.826, 125.826, 37.013
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
DetailsA and B, C and D from PISA

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Components

#1: Protein
DNA-entry nuclease inhibitor / Competence protein J


Mass: 15472.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: nin, comJ, BSU03420 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pGrow7-K / References: UniProt: P12669
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M sodium acetate pH 4.5, 20% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2013
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 35143 / Num. obs: 35026 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 12.3
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.974 / Mean I/σ(I) obs: 1.54 / Num. unique all: 1786 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SBC-CollectCOLLECTdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
ARP/wARPmodel building
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.16→41.22 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.221 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.225
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 1514 5.1 %RANDOM
Rwork0.1779 ---
all0.1811 29654 --
obs0.1811 29654 83.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.42 Å2 / Biso mean: 36.687 Å2 / Biso min: 11.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.2 Å2-0 Å2
2---0.2 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.16→41.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4234 0 0 269 4503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0194406
X-RAY DIFFRACTIONr_bond_other_d0.0010.024055
X-RAY DIFFRACTIONr_angle_refined_deg0.8451.9465991
X-RAY DIFFRACTIONr_angle_other_deg0.57139391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2135540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.33424.925201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.80615695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3031513
X-RAY DIFFRACTIONr_chiral_restr0.0550.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0214961
X-RAY DIFFRACTIONr_gen_planes_other00.02996
X-RAY DIFFRACTIONr_rigid_bond_restr0.49738461
X-RAY DIFFRACTIONr_sphericity_free32.9555122
X-RAY DIFFRACTIONr_sphericity_bonded12.71158495
LS refinement shellResolution: 2.156→2.212 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 8 -
Rwork0.267 131 -
all-139 -
obs-139 5.23 %

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