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- PDB-4ayn: Structure of the C-terminal barrel of Neisseria meningitidis FHbp... -

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Basic information

Entry
Database: PDB / ID: 4ayn
TitleStructure of the C-terminal barrel of Neisseria meningitidis FHbp Variant 2
ComponentsFACTOR H-BINDING PROTEIN
KeywordsIMMUNE SYSTEM / ANTIGENS / COMPLEMENT FACTOR H / VACCINES
Function / homologyFactor H binding protein, C-terminal / Factor H binding protein, C-terminal / Porin - #90 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / cell outer membrane / Beta Barrel / Mainly Beta / Factor H-binding protein
Function and homology information
Biological speciesNEISSERIA MENINGITIDIS MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsJohnson, S. / Tan, L. / van der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Everett, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. ...Johnson, S. / Tan, L. / van der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Everett, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. / Trivedi, K. / Cumber, E. / Jones, R. / Newham, L. / Staunton, D. / Borrow, R. / Pickering, M. / Lea, S.M. / Tang, C.M.
CitationJournal: Plos Pathog. / Year: 2012
Title: Design and Evaluation of Meningococcal Vaccines Through Structure-Based Modification of Host and Pathogen Molecules.
Authors: Johnson, S. / Tan, L. / Van Der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Harding, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. / Trivedi, K. / Cumber, E. / Jones, R. / ...Authors: Johnson, S. / Tan, L. / Van Der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Harding, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. / Trivedi, K. / Cumber, E. / Jones, R. / Newham, L. / Staunton, D. / Ufret-Vincenty, R. / Borrow, R. / Pickering, M.C. / Lea, S.M. / Tang, C.M.
History
DepositionJun 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Mar 25, 2015Group: Database references / Source and taxonomy
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FACTOR H-BINDING PROTEIN
B: FACTOR H-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,94611
Polymers59,0822
Non-polymers8659
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-134 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.791, 75.951, 40.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.31355, -0.94855, -0.04401), (-0.94957, -0.31335, -0.01146), (-0.00292, 0.04538, -0.99897)
Vector: 51.22273, 70.93513, -5.31968)

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Components

#1: Protein FACTOR H-BINDING PROTEIN / FACTOR H BINDING PROTEIN V2


Mass: 29540.922 Da / Num. of mol.: 2 / Fragment: RESIDUES 27-273
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS MC58 (bacteria) / Variant: P22 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: C6KHT4
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDISCREPANCIES AT TERMINI ARE FROM VECTOR. THE SEQUENCE HAS BEEN RENUMBERED TO MATCH THAT OF THE ...DISCREPANCIES AT TERMINI ARE FROM VECTOR. THE SEQUENCE HAS BEEN RENUMBERED TO MATCH THAT OF THE VARIANT 1 SEQUENCE (PDB ID 2W81)

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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: 2.05 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 4.6
Details: 30% PEG2KMME, 0.1 M SODIUM ACETATE PH 4.6, 0.2 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.06→60 Å / Num. obs: 14737 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 32.19 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26
Reflection shellResolution: 2.06→2.18 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 6.8 / % possible all: 91.3

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W81

2w81


Resolution: 2.06→15 Å / Cor.coef. Fo:Fc: 0.9491 / Cor.coef. Fo:Fc free: 0.9296 / SU R Cruickshank DPI: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.224 / SU Rfree Blow DPI: 0.168 / SU Rfree Cruickshank DPI: 0.164
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 741 5.03 %RANDOM
Rwork0.1788 ---
obs0.1805 14737 98.64 %-
Displacement parametersBiso mean: 32.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.6616 Å20 Å20 Å2
2---5.826 Å20 Å2
3---5.1644 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.06→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 45 120 2060
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011970HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.122649HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d687SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes53HARMONIC2
X-RAY DIFFRACTIONt_gen_planes287HARMONIC5
X-RAY DIFFRACTIONt_it1970HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.83
X-RAY DIFFRACTIONt_other_torsion17.05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion241SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2222SEMIHARMONIC4
LS refinement shellResolution: 2.06→2.23 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2327 146 5.15 %
Rwork0.1943 2687 -
all0.1962 2833 -
obs--98.64 %

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