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- PDB-4fc3: Crystal Structure of Human Methaemoglobin Complexed with the Seco... -

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Basic information

Entry
Database: PDB / ID: 4fc3
TitleCrystal Structure of Human Methaemoglobin Complexed with the Second NEAT Domain of IsdH from Staphylococcus aureus
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
  • Iron-regulated surface determinant protein H
KeywordsOXYGEN TRANSPORT/PROTEIN BINDING / Globin Fold / Ig Fold / Oxygen Transport / Haem acquisition / Oxygen Binding / Haem binding / cell wall / OXYGEN TRANSPORT-PROTEIN BINDING complex
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / Late endosomal microautophagy / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / response to hydrogen peroxide / platelet aggregation / oxygen binding / regulation of blood pressure / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
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 / : ...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 / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha / Iron-regulated surface determinant protein H
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 Å
AuthorsKrishna Kumar, K. / Jacques, D.A. / Guss, J.M. / Gell, D.A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure of the Hemoglobin-IsdH Complex Reveals the Molecular Basis of Iron Capture by Staphylococcus aureus
Authors: Dickson, C.F. / Krishna Kumar, K. / Jacques, D.A. / Malmirchegini, G.R. / Spirig, T. / Mackay, J.P. / Clubb, R.T. / Guss, J.M. / Gell, D.A.
History
DepositionMay 24, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Oct 28, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: 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: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
E: Iron-regulated surface determinant protein H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0825
Polymers49,8493
Non-polymers1,2332
Water54030
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
E: Iron-regulated surface determinant protein H
hetero molecules

A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
E: Iron-regulated surface determinant protein H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,16510
Polymers99,6996
Non-polymers2,4664
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Unit cell
Length a, b, c (Å)67.041, 149.581, 86.265
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Hemoglobin subunit alpha / Alpha-globin / Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain / LVV-hemorphin-7


Mass: 15890.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871
#3: Protein Iron-regulated surface determinant protein H / Haptoglobin receptor A / Staphylococcus aureus surface protein I


Mass: 18808.891 Da / Num. of mol.: 1 / Fragment: Second NEAT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MW2 / Gene: isdH / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NW39
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.17 Å3/Da / Density % sol: 43.3 % / Mosaicity: 1.144 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Sodium formate, 0.1M bis-tris propane, 20% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2011
RadiationMonochromator: Double crystal (Si111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. all: 19451 / Num. obs: 19451 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.122 / Χ2: 1.071 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.26-2.33.50.5739841.2197
2.3-2.343.80.499971.114197.1
2.34-2.393.80.459651.137196.8
2.39-2.433.70.4859881.267197.7
2.43-2.493.80.36910031.065197.3
2.49-2.553.90.3539731.111196.5
2.55-2.613.90.3259881.118196.6
2.61-2.683.90.2999811.094197
2.68-2.763.90.2549921.035196.6
2.76-2.853.90.2359810.999196.7
2.85-2.9540.1929861.076196.3
2.95-3.0740.1669781.064195.8
3.07-3.2140.1429891.05195.8
3.21-3.3840.1229921.016196.3
3.38-3.593.90.1059811.074195.2
3.59-3.863.30.1147871.083176.3
3.86-4.253.80.0839661.027192.4
4.25-4.873.50.0799010.913186.1
4.87-6.133.90.079911.072192.9
6.13-503.90.06110280.923191

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 50.11 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.9 Å
Translation2.5 Å49.9 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3szk

3szk


Resolution: 2.26→49.9 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.281 / WRfactor Rwork: 0.2474 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8265 / SU B: 16.721 / SU ML: 0.185 / SU R Cruickshank DPI: 0.4378 / SU Rfree: 0.2598 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.438 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 993 5.1 %RANDOM
Rwork0.219 ---
obs0.2209 19351 93.22 %-
all-19351 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 46.25 Å2 / Biso mean: 34.361 Å2 / Biso min: 3.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2---0.95 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.26→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 86 30 3408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223477
X-RAY DIFFRACTIONr_bond_other_d0.0010.022245
X-RAY DIFFRACTIONr_angle_refined_deg0.762.0284760
X-RAY DIFFRACTIONr_angle_other_deg0.73835501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3945424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39424.507142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.7315534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.87159
X-RAY DIFFRACTIONr_chiral_restr0.0450.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213847
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02665
X-RAY DIFFRACTIONr_mcbond_it0.63622129
X-RAY DIFFRACTIONr_mcbond_other0.1192854
X-RAY DIFFRACTIONr_mcangle_it1.23233422
X-RAY DIFFRACTIONr_scbond_it1.85541348
X-RAY DIFFRACTIONr_scangle_it3.03361338
LS refinement shellResolution: 2.259→2.318 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 66 -
Rwork0.268 1249 -
all-1315 -
obs--86.91 %
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)
11.335-0.425-0.62831.9129-0.02921.32810.0495-0.1659-0.00610.1151-0.082-0.0642-0.00770.05610.03250.0169-0.0194-0.01560.06130.01110.03137.8448-29.6503-8.4586
21.84280.4329-0.452.4567-0.11322.49850.0125-0.0520.0573-0.042-0.0661-0.0942-0.22450.14390.05360.0378-0.02820.0120.0390.01140.068217.1545-13.2169-22.7762
31.96110.61840.34022.9990.04122.1784-0.0810.0594-0.14130.01510.08230.02560.0656-0.0126-0.00130.03710.0190.00010.0186-0.00880.023516.7969-57.2752-16.1459
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 140
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION2B1 - 143
4X-RAY DIFFRACTION2B201
5X-RAY DIFFRACTION3E1 - 144

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