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- PDB-4q7o: The crystal structure of an immunity protein NMB0503 from Neisser... -

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Basic information

Entry
Database: PDB / ID: 4q7o
TitleThe crystal structure of an immunity protein NMB0503 from Neisseria meningitidis MC58
ComponentsImmunity protein
KeywordsIMMUNE SYSTEM / structural genomics / PSI-Biology / protein structure initiative / MCSG / Midwest Center for Structural Genomics / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes / UC4CDI
Function / homologyBROMIDE ION / FORMIC ACID / CDI immunity protein domain-containing protein
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsTan, K. / Stols, L. / Eschenfeldt, W. / Babnigg, G. / Low, D.A. / Hayes, C.S. / Goulding, C.W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: The structure of a contact-dependent growth-inhibition (CDI) immunity protein from Neisseria meningitidis MC58.
Authors: Tan, K. / Johnson, P.M. / Stols, L. / Boubion, B. / Eschenfeldt, W. / Babnigg, G. / Hayes, C.S. / Joachimiak, A. / Goulding, C.W.
History
DepositionApr 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Feb 28, 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

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Assembly

Deposited unit
A: Immunity protein
B: Immunity protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,12917
Polymers34,0322
Non-polymers1,09715
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-18 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.383, 53.532, 59.699
Angle α, β, γ (deg.)90.00, 98.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Immunity protein


Mass: 17016.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMB0503 / Plasmid: pMCSG58 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q7DDN8
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M MgCl, 0.1M Bis-Tris:HCl, 25% (w/v) PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91928 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2013 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91928 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. all: 49973 / Num. obs: 49973 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 3.4 % / Biso Wilson estimate: 10.34 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 24.4
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.76 / Num. unique all: 2352 / % possible all: 94.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→29.556 Å / SU ML: 0.12 / σ(F): 1.35 / Phase error: 16.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.189 2544 5.09 %random
Rwork0.1488 ---
obs0.1508 49934 99.31 %-
all-49934 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→29.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2207 0 21 279 2507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052303
X-RAY DIFFRACTIONf_angle_d0.9673123
X-RAY DIFFRACTIONf_dihedral_angle_d12.735831
X-RAY DIFFRACTIONf_chiral_restr0.07336
X-RAY DIFFRACTIONf_plane_restr0.004401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.47830.24171400.18292440X-RAY DIFFRACTION93
1.4783-1.50850.2221300.16552635X-RAY DIFFRACTION100
1.5085-1.54130.21111330.14752636X-RAY DIFFRACTION100
1.5413-1.57720.18171470.13262646X-RAY DIFFRACTION100
1.5772-1.61660.16371630.12412619X-RAY DIFFRACTION100
1.6166-1.66030.17121340.12232648X-RAY DIFFRACTION100
1.6603-1.70910.17831580.12262602X-RAY DIFFRACTION100
1.7091-1.76430.17461230.12552645X-RAY DIFFRACTION100
1.7643-1.82740.18831280.13142662X-RAY DIFFRACTION100
1.8274-1.90050.20071570.1312637X-RAY DIFFRACTION100
1.9005-1.9870.18251370.1312665X-RAY DIFFRACTION100
1.987-2.09170.17281320.13492625X-RAY DIFFRACTION100
2.0917-2.22270.18591330.13382669X-RAY DIFFRACTION100
2.2227-2.39430.18941540.13962646X-RAY DIFFRACTION100
2.3943-2.63510.18341610.15782625X-RAY DIFFRACTION100
2.6351-3.01610.19251390.16822657X-RAY DIFFRACTION99
3.0161-3.79870.20111530.16322650X-RAY DIFFRACTION99
3.7987-29.56240.18411220.16892683X-RAY DIFFRACTION97

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