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- PDB-3h8t: Structure of Porphyromonas gingivalis heme-binding protein HmuY i... -

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Basic information

Entry
Database: PDB / ID: 3h8t
TitleStructure of Porphyromonas gingivalis heme-binding protein HmuY in complex with Heme
ComponentsHmuY
Keywordsheme-binding protein / hemophore / bacterial virulence factor / periodontitis
Function / homologyHmuY protein / HmuY protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / HmuY
Function and homology information
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsWojtowicz, H. / Guevara, T. / Tallant, C. / Olczak, M. / Sroka, A. / Potempa, J. / Sola, M. / Olczak, T. / Gomis-Ruth, F.X.
CitationJournal: Plos Pathog. / Year: 2009
Title: Unique structure and stability of HmuY, a novel heme-binding protein of Porphyromonas gingivalis
Authors: Wojtowicz, H. / Guevara, T. / Tallant, C. / Olczak, M. / Sroka, A. / Potempa, J. / Sola, M. / Olczak, T. / Gomis-Ruth, F.X.
History
DepositionApr 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 14, 2012Group: Refinement description
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: HmuY
B: HmuY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,62514
Polymers42,4552
Non-polymers2,17012
Water7,782432
1
A: HmuY
B: HmuY
hetero molecules

A: HmuY
B: HmuY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,25028
Polymers84,9104
Non-polymers4,34024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area13790 Å2
ΔGint-245 kcal/mol
Surface area30920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.740, 93.740, 113.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein HmuY


Mass: 21227.529 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 26 TO 216 (26 to 34 disordered)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: HmuY, hmuY' / Production host: Escherichia coli (E. coli) / References: UniProt: A2I2W2
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Crystallization assays were performed following the sitting-drop vapor diffusion method. Reservoir solutions were prepared by a Tecan robot and 200-nL crystallization drops were dispensed on ...Details: Crystallization assays were performed following the sitting-drop vapor diffusion method. Reservoir solutions were prepared by a Tecan robot and 200-nL crystallization drops were dispensed on 96x2-well MRC plates (Wilden / Innovadyne) by a Cartesian nanodrop robot (Genomic Solutions) at the joint IBMB-CSIC/IRB/Barcelona Science Park High-Throughput Crystallography Platform (PAC). Best crystals as thin reddish prisms appeared in a Bruker steady-temperature crystal farm at 20 C using protein solution (26mg/mL in 5mM Tris/HCl, pH 8.0) and 2.4M (NH4)2SO4, 0.1M MES, pH6.0 as reservoir solution and D(+)-glucose monohydrate as additive (relative volumetric ratios 1:1:0.35). These conditions were successfully scaled up to the microliter range with Cryschem crystallization dishes (Hampton Research). VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-111
SYNCHROTRONESRF ID23-120.9792
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJul 18, 2008
ADSC QUANTUM 315r2CCDOct 27, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Silicon (1 1 1) channel-cutSINGLE WAVELENGTHMx-ray1
2Silicon (1 1 1) channel-cutSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97921
ReflectionResolution: 1.8→48.6 Å / Num. all: 47598 / Num. obs: 47598 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 17.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 4.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDEphasing
REFMAC5.5.0046refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→48.6 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.29 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18709 720 1.5 %RANDOM
Rwork0.16015 ---
obs0.16057 46847 99.95 %-
all-47598 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.133 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 142 432 3432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223084
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.312.0384188
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6335362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86524.571140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49215489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6151511
X-RAY DIFFRACTIONr_chiral_restr0.1050.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212351
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_it0.6951.51790
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32522876
X-RAY DIFFRACTIONr_scbond_it2.18831294
X-RAY DIFFRACTIONr_scangle_it3.6084.51312
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 58 -
Rwork0.2 3403 -
obs--99.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.32270.22140.08860.592-0.11950.1811-0.02240.0577-0.06050.02790.0382-0.0915-0.0032-0.0398-0.01580.0546-0.02310.00520.0506-0.00530.0421-6.06327.96629.321
21.83861.82380.9781.82060.6977.5605-0.03210.218-0.1896-0.05690.2503-0.18140.0010.0606-0.21820.0754-0.02920.01830.1101-0.0280.0579-1.05139.90415.654
30.41420.1198-0.14370.5756-0.26670.31960.0202-0.01490.0390.04360.0028-0.0249-0.0278-0.0071-0.02310.0597-0.00860.00260.03710.00160.02962.95166.472-10.97
40.2627-0.90620.65775.31630.48485.1299-0.0496-0.09020.02970.21780.277-0.33-0.1141-0.2885-0.22740.0993-0.0055-0.01920.0764-0.00820.06752.09553.5752.829
50.05290.1064-0.13250.2831-0.31880.4334-0.0040.0099-0.010.0207-0.0081-0.046-0.0244-0.02080.01210.067-0.0107-0.00250.0626-0.00740.0669-0.71846.78710.413
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 216
2X-RAY DIFFRACTION2A301
3X-RAY DIFFRACTION3B35 - 216
4X-RAY DIFFRACTION4B301
5X-RAY DIFFRACTION5A511 - 938
6X-RAY DIFFRACTION5B534 - 942

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