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- PDB-6ewm: Crystal structure of heme free PORPHYROMONAS GINGIVALIS HEME-BIND... -

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Basic information

Entry
Database: PDB / ID: 6ewm
TitleCrystal structure of heme free PORPHYROMONAS GINGIVALIS HEME-BINDING PROTEIN HMUY
ComponentsHaemophore HmuY
KeywordsCELL INVASION / heme-binding protein
Function / homologyHmuY protein / HmuY protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / HmuY
Function and homology information
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAntonyuk, S.V. / Strange, R.W. / Bielecki, M. / Olczak, T. / Olczak, M.
Funding support Poland, 2items
OrganizationGrant numberCountry
National Science Center2015/17/B/NZ6/01969 Poland
European Regional Development FundPOIG 01.01.02-02-003/08/00 Poland
CitationJournal: Biosci. Rep. / Year: 2018
Title: Tannerella forsythiaTfo belongs toPorphyromonas gingivalisHmuY-like family of proteins but differs in heme-binding properties.
Authors: Bielecki, M. / Antonyuk, S. / Strange, R.W. / Smalley, J.W. / Mackiewicz, P. / Smiga, M. / Stepien, P. / Olczak, M. / Olczak, T.
History
DepositionNov 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Haemophore HmuY
F: Haemophore HmuY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,68714
Polymers42,4552
Non-polymers1,23212
Water13,169731
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-60 kcal/mol
Surface area17390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.334, 42.947, 95.075
Angle α, β, γ (deg.)90.00, 107.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Haemophore HmuY / HmuY / HmuY protein


Mass: 21227.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria)
Gene: hmuY', hmuY, AT291_03715, PGIN_13-1_01941, PGIN_YH522_00859
Plasmid: pHmuY11 / Production host: Escherichia coli (E. coli) / References: UniProt: A2I2W2
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 2.4 M ammonium sulphate, 100 mM MES pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2017
RadiationMonochromator: si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.4→90.9 Å / Num. obs: 86584 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 4.3 % / CC1/2: 0.98 / Rmerge(I) obs: 0.014 / Rpim(I) all: 0.01 / Net I/σ(I): 5.9
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3231 / CC1/2: 0.68 / Rpim(I) all: 0.43 / % possible all: 74

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3h8t

3h8t


Resolution: 1.4→90.49 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.874 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.053 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17102 4266 4.9 %RANDOM
Rwork0.13126 ---
obs0.13323 82229 95.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.467 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å2-0.01 Å2
2---0.41 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.4→90.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 72 731 3671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023085
X-RAY DIFFRACTIONr_bond_other_d0.0020.022815
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9554178
X-RAY DIFFRACTIONr_angle_other_deg0.91236523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8795388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42624.825143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.14115512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4191510
X-RAY DIFFRACTIONr_chiral_restr0.10.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023504
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02714
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2931.0271498
X-RAY DIFFRACTIONr_mcbond_other1.2791.0261497
X-RAY DIFFRACTIONr_mcangle_it1.6121.5521880
X-RAY DIFFRACTIONr_mcangle_other1.6151.5521881
X-RAY DIFFRACTIONr_scbond_it2.0571.3331587
X-RAY DIFFRACTIONr_scbond_other2.0561.3331587
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4371.8922291
X-RAY DIFFRACTIONr_long_range_B_refined4.69112.2174138
X-RAY DIFFRACTIONr_long_range_B_other3.35510.1683674
X-RAY DIFFRACTIONr_rigid_bond_restr1.62535900
X-RAY DIFFRACTIONr_sphericity_free35.3285199
X-RAY DIFFRACTIONr_sphericity_bonded9.52956379
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 257 -
Rwork0.177 4741 -
obs--75.21 %

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