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- PDB-3szk: Crystal Structure of Human metHaemoglobin Complexed with the Firs... -

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Basic information

Entry
Database: PDB / ID: 3szk
TitleCrystal Structure of Human metHaemoglobin Complexed with the First NEAT Domain of IsdH from Staphylococcus aureus
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
  • Iron-regulated surface determinant protein H
KeywordsOXYGEN TRANSPORT/PROTEIN BINDING / methaemoglobin / NEAT domain / IsdH / host-pathogen interaction / OXYGEN TRANSPORT-PROTEIN BINDING complex
Function / homology
Function and homology information


nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin 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 / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / 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 / Hemoglobin, pi ...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 / Hemoglobin, pi / YSIRK Gram-positive signal peptide / 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 / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsJacques, D.A. / Kumar, K.K. / Guss, J.M. / Gell, D.A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural basis for hemoglobin capture by Staphylococcus aureus cell-surface protein, IsdH
Authors: Krishna Kumar, K. / Jacques, D.A. / Pishchany, G. / Caradoc-Davies, T. / Spirig, T. / Malmirchegini, G.R. / Langley, D.B. / Dickson, C.F. / Mackay, J.P. / Clubb, R.T. / Skaar, E.P. / Guss, J.M. / Gell, D.A.
History
DepositionJul 19, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Nov 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_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 / _struct_ref_seq_dif.details / _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
D: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
E: Hemoglobin subunit beta
F: Iron-regulated surface determinant protein H
A: Hemoglobin subunit alpha
C: Iron-regulated surface determinant protein H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,35710
Polymers99,8916
Non-polymers2,4664
Water00
1
D: Hemoglobin subunit alpha
E: Hemoglobin subunit beta
F: Iron-regulated surface determinant protein H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1785
Polymers49,9453
Non-polymers1,2332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-56 kcal/mol
Surface area19560 Å2
MethodPISA
2
B: Hemoglobin subunit beta
A: Hemoglobin subunit alpha
C: Iron-regulated surface determinant protein H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1785
Polymers49,9453
Non-polymers1,2332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-56 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.880, 123.206, 143.933
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
11B
21A
12E
22F
13C
23D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISHISHIS4BB2 - 1432 - 143
21VALVALTYRTYR4AE1 - 1401 - 140
12THRTHRALAALA5EC12 - 14212 - 142
22SERSERLEULEU5FD89 - 22924 - 164
13ALAALALEULEU4CF86 - 22921 - 164
23VALVALTYRTYR4DA1 - 1401 - 140

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 15150.353 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871
#3: Protein Iron-regulated surface determinant protein H / IsdH / Haptoglobin receptor A / Staphylococcus aureus surface protein I


Mass: 18904.824 Da / Num. of mol.: 2 / Fragment: first NEAT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MW2 / Plasmid: pET11a / 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.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M potassium thiocyanate, 0.1M Tris-bis propane, 20% PEG 3350 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 2, 2011
RadiationMonochromator: OSMIC VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.007→48.59 Å / Num. obs: 22644 / % possible obs: 95.76 %
Reflection shellResolution: 3.007→3.085 Å / % possible all: 99.58

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DN1, 3OVU

2dn1

3ovu


Resolution: 3.01→48.59 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.845 / SU B: 49.675 / SU ML: 0.395 / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27539 1224 5.1 %RANDOM
Rwork0.24523 ---
obs0.2468 22644 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.914 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2--0.51 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 3.01→48.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6434 0 172 0 6606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0226797
X-RAY DIFFRACTIONr_bond_other_d0.0010.024371
X-RAY DIFFRACTIONr_angle_refined_deg0.6982.0319306
X-RAY DIFFRACTIONr_angle_other_deg0.71310724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6825823
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.82924.844289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.536151048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.2341516
X-RAY DIFFRACTIONr_chiral_restr0.0410.21015
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217569
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021283
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_it2.69924143
X-RAY DIFFRACTIONr_mcbond_other0.59821654
X-RAY DIFFRACTIONr_mcangle_it4.62836663
X-RAY DIFFRACTIONr_scbond_it6.63842654
X-RAY DIFFRACTIONr_scangle_it9.68962643
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A143MEDIUM POSITIONAL2.610.5
1A143MEDIUM THERMAL0.132
2E40MEDIUM POSITIONAL4.670.5
2E38LOOSE POSITIONAL5.035
2E40MEDIUM THERMAL0.182
2E38LOOSE THERMAL0.1110
3C20MEDIUM POSITIONAL0.410.5
3C20MEDIUM THERMAL0.132
LS refinement shellResolution: 3.007→3.085 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 84 -
Rwork0.374 1542 -
obs--99.58 %
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)
13.4475-0.18120.88863.32120.90493.3871-0.0499-0.37530.11650.2736-0.06060.2337-0.1489-0.44860.11050.0910.04910.01750.1278-0.03020.056541.119946.7285-43.4673
24.2349-1.2381-2.42724.62540.57846.75050.2276-0.9381-0.41820.3916-0.03130.3252-0.12440.0885-0.19630.2344-0.10440.01010.30880.16810.165448.696128.3315-29.9649
32.8258-0.03890.984.3613-1.50853.4080.1450.3105-0.1015-0.3839-0.3159-0.11130.3528-0.1630.17090.2350.0773-0.01470.1696-0.10940.20238.765639.6531-73.0442
42.88860.41130.92794.13151.54163.4689-0.25590.34560.1909-0.99240.3039-0.1521-0.6538-0.026-0.0480.3937-0.21270.03410.2970.00820.085431.35128.58657.3587
53.089-2.8259-0.52628.5149-1.31777.07610.05610.26330.2598-1.21640.3865-1.0831-0.14180.6283-0.44260.54-0.44250.450.6106-0.25760.508750.35980.0436-4.3324
64.05670.1435-1.37913.39431.2714.0226-0.22290.03660.00880.05470.283-0.2597-0.00330.4168-0.06010.09810.0254-0.09790.147-0.10880.243938.42410.950836.9925
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 140
2X-RAY DIFFRACTION2B2 - 143
3X-RAY DIFFRACTION3C86 - 229
4X-RAY DIFFRACTION4D1 - 140
5X-RAY DIFFRACTION5E12 - 142
6X-RAY DIFFRACTION6F89 - 229

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