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- PDB-3quh: Structure of heme transport protein IsdH-NEAT3 from S. aureus in ... -

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Basic information

Entry
Database: PDB / ID: 3quh
TitleStructure of heme transport protein IsdH-NEAT3 from S. aureus in complex with Manganese(III)-porphyrin
ComponentsIron-regulated surface determinant protein H
KeywordsHEME-BINDING PROTEIN / Manganese (III) / Metalloporphyrin / Metal Selectivity / NEAT Domain / Heme Binding / Heme Transport / Heme / Hemin / PPIX / protoporphyrin IX / Cell Wall
Function / homology
Function and homology information


heme binding / extracellular region
Similarity search - Function
Iron-regulated surface determinant protein H / : / Iron-regulated surface determinant protein H/B, linker domain / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / YSIRK type signal peptide ...Iron-regulated surface determinant protein H / : / Iron-regulated surface determinant protein H/B, linker domain / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING MN / Iron-regulated surface determinant protein H
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsMoriwaki, Y. / Caaveiro, J.M.M. / Tsumoto, K.
Citation
Journal: Biochemistry / Year: 2011
Title: Molecular basis of recognition of antibacterial porphyrins by heme-transporter IsdH-NEAT3 of Staphylococcus aureus.
Authors: Moriwaki, Y. / Caaveiro, J.M.M. / Tanaka, Y. / Tsutsumi, H. / Hamachi, I. / Tsumoto, K.
#1: Journal: J.Biol.Chem. / Year: 2008
Title: Structural basis for multimeric heme complexation through a specific protein-heme interaction: the case of the third neat domain of IsdH from Staphylococcus aureus.
Authors: Watanabe, M. / Tanaka, Y. / Suenaga, A. / Kuroda, M. / Yao, M. / Watanabe, N. / Arisaka, F. / Ohta, T. / Tanaka, I. / Tsumoto, K.
History
DepositionFeb 24, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 15, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: Iron-regulated surface determinant protein H
B: Iron-regulated surface determinant protein H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2896
Polymers28,8742
Non-polymers1,4154
Water59433
1
A: Iron-regulated surface determinant protein H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1453
Polymers14,4371
Non-polymers7082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Iron-regulated surface determinant protein H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1453
Polymers14,4371
Non-polymers7082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.280, 75.930, 49.330
Angle α, β, γ (deg.)90.000, 95.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Iron-regulated surface determinant protein H / Haptoglobin receptor A / Staphylococcus aureus surface protein I


Mass: 14437.006 Da / Num. of mol.: 2 / Fragment: NEAT Domain (UNP REIDUES 539-664)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: harA, isdH, IsdH-NEAT3, sasI, SAV1731 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q931P4
#2: Chemical ChemComp-MNR / PROTOPORPHYRIN IX CONTAINING MN


Mass: 615.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32MnN4O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.67 Å3/Da / Density % sol: 53.88 % / Mosaicity: 2.17 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG-MME 500 30%, Bicine 0.1M, Sodium Chloride 0.1M, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 10, 2010 / Details: mirror
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→49.14 Å / Num. all: 8138 / Num. obs: 8138 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rsym value: 0.142 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.7-2.853.30.4810.4041.9386411710.2580.4810.4042.897
2.85-3.023.30.3260.2742.8370611320.1740.3260.274496.8
3.02-3.233.30.2350.1983.8347110550.1260.2350.1985.196.9
3.23-3.493.30.1640.1385.232109810.0880.1640.1386.896.4
3.49-3.823.30.1530.1285.529378880.0820.1530.1287.995.9
3.82-4.273.30.1320.1116.426878200.0710.1320.1118.997.1
4.27-4.933.20.1040.0877.923397250.0560.1040.08710.297.2
4.93-6.043.20.1070.097.420326270.0580.1070.09997
6.04-8.543.20.120.16.315224740.0650.120.17.595.9
8.54-36.15630.0990.0826.97952650.0540.0990.08210.395.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.01 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å36.16 Å
Translation2.7 Å36.16 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z6F

2z6f


Resolution: 2.7→49.14 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.824 / WRfactor Rfree: 0.2756 / WRfactor Rwork: 0.2137 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7464 / SU B: 37.012 / SU ML: 0.351 / SU R Cruickshank DPI: 0.324 / SU Rfree: 0.3979 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28621 373 4.6 %RANDOM
Rwork0.22439 ---
obs0.22732 7754 96.61 %-
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 max: 70.35 Å2 / Biso mean: 38.433 Å2 / Biso min: 20.19 Å2
Baniso -1Baniso -2Baniso -3
1-3.85 Å20 Å20.39 Å2
2---1.48 Å20 Å2
3----2.3 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 98 33 1947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221966
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.232.0812694
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.96425.21792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.38215320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.216156
X-RAY DIFFRACTIONr_chiral_restr0.080.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211492
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_it0.2871.51116
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.54521830
X-RAY DIFFRACTIONr_scbond_it0.8423850
X-RAY DIFFRACTIONr_scangle_it1.4494.5864
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 20 -
Rwork0.269 574 -
all-594 -
obs--97.22 %
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)
10.65370.4765-0.66184.8011-0.8633.04690.0536-0.018-0.22960.0219-0.0621-0.2924-0.01890.00480.00850.2367-0.01070.01480.1285-0.01210.116619.2392-53.889144.2627
21.1043-0.4619-0.14896.4461-0.6272.0381-0.06050.11870.12240.03560.0269-0.1898-0.02350.0470.03370.30020.0185-0.00930.1105-0.00050.019220.5866-23.781729.8303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A544 - 655
2X-RAY DIFFRACTION2B544 - 655

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