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- PDB-6r2h: Crystal structure of Apo PinO from Porphyromonas gingivitis -

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Basic information

Entry
Database: PDB / ID: 6r2h
TitleCrystal structure of Apo PinO from Porphyromonas gingivitis
ComponentsHmuY protein
KeywordsMETAL BINDING PROTEIN / Porphyromonas gingivalis / Prevotella intermedia / HmuY / heme / hemophore / heme-binding protein / phylogeny / sequence evolution
Function / homologyHmuY protein / HmuY protein / HmuY protein
Function and homology information
Biological speciesPrevotella intermedia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsAntonyuk, S.V. / Bielecki, M. / Strange, R.W. / Capper, M. / Olczak, T. / Olczak, M.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science Centre2015/17/B/NZ6/01969 Poland
European Regional Development FundPOIG 01.01.02-02-003/08/00 Poland
CitationJournal: Biochem.J. / Year: 2020
Title: Prevotella intermedia produces two proteins homologous to Porphyromonas gingivalis HmuY but with different heme coordination mode.
Authors: Bielecki, M. / Antonyuk, S. / Strange, R.W. / Sieminska, K. / Smalley, J.W. / Mackiewicz, P. / Smiga, M. / Cowan, M. / Capper, M.J. / Slezak, P. / Olczak, M. / Olczak, T.
History
DepositionMar 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 21, 2022Group: Data collection / Database references / Refinement description
Category: database_2 / reflns / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _reflns.pdbx_CC_half / _software.name
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,7205
Polymers43,4442
Non-polymers2763
Water2,954164
1
A: HmuY protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9063
Polymers21,7221
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HmuY protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8142
Polymers21,7221
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.254, 54.102, 161.091
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 3 - 192 / Label seq-ID: 3 - 192

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein HmuY protein


Mass: 21722.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prevotella intermedia (bacteria) / Gene: BWX40_10235 / Cell line (production host): DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1P8JNE7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 25% PEG MED SMEAR

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91787 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 15, 2017 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91787 Å / Relative weight: 1
ReflectionResolution: 2.458→80.546 Å / Num. obs: 14071 / % possible obs: 97.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 36.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.135 / Rrim(I) all: 0.147 / Net I/σ(I): 0.147
Reflection shellResolution: 2.458→2.501 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.934 / Mean I/σ(I) obs: 2 / Num. unique obs: 4715 / CC1/2: 0.817 / Rpim(I) all: 0.533 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EU8

6eu8


Resolution: 2.46→80.546 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 12.358 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.884 / ESU R Free: 0.283 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23328 649 4.6 %RANDOM
Rwork0.19419 ---
obs0.19595 13422 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.19 Å2
Baniso -1Baniso -2Baniso -3
1--2.46 Å20 Å20 Å2
2--4.08 Å20 Å2
3----1.62 Å2
Refinement stepCycle: 1 / Resolution: 2.46→80.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 18 164 3117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123005
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.6424032
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9225371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9124.745137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.42115562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.097158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022222
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.664.0651496
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.2766.0761863
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4544.3371509
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.65553.3214293
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5285 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.458→2.522 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 56 -
Rwork0.325 983 -
obs--99.81 %

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