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- PDB-3ovu: Crystal Structure of Human Alpha-Haemoglobin Complexed with AHSP ... -

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Basic information

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


hemoglobin metabolic process / cellular oxidant detoxification / nitric oxide transport / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid binding / hemoglobin complex / hemopoiesis / oxygen transport / Scavenging of heme from plasma ...hemoglobin metabolic process / cellular oxidant detoxification / nitric oxide transport / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid binding / hemoglobin complex / hemopoiesis / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / erythrocyte differentiation / hydrogen peroxide catabolic process / oxygen carrier activity / Heme signaling / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / unfolded protein binding / protein folding / blood microparticle / protein stabilization / iron ion binding / heme binding / extracellular space / extracellular exosome / extracellular region / membrane / cytosol / cytoplasm
Similarity search - Function
Alpha-haemoglobin stabilising protein / AHSP superfamily / Alpha-haemoglobin stabilising protein / AHSP / Iron-regulated surface determinant protein H / : / Iron-regulated surface determinant protein H/B, linker domain / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain ...Alpha-haemoglobin stabilising protein / AHSP superfamily / Alpha-haemoglobin stabilising protein / AHSP / 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 / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Globin/Protoglobin / Globins / Globin domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Globin-like / Globin / Globin / Globin-like superfamily / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha / Iron-regulated surface determinant protein H / Alpha-hemoglobin-stabilizing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.83 Å
AuthorsJacques, D.A. / Krishna Kumar, K. / Caradoc-Davies, T.T. / Langley, D.B. / Mackay, J.P. / Guss, J.M. / Gell, D.A.
CitationJournal: To be Published
Title: A new haem pocket structure in alpha-haemoglobin
Authors: Krishna Kumar, K. / Jacques, D.A. / Caradoc-Davies, T.T. / Spirig, T. / Langley, D.B. / Mackay, J.P. / Guss, J.M. / Clubb, R.T. / Gell, D.A.
History
DepositionSep 17, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_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
A: Alpha-hemoglobin-stabilizing protein
B: Iron-regulated surface determinant protein H
C: Hemoglobin subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3934
Polymers45,7763
Non-polymers6161
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-20 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.638, 71.659, 82.058
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha-hemoglobin-stabilizing protein / Erythroid-associated factor / Erythroid differentiation-related factor


Mass: 11721.169 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AHSP / Plasmid: pGEX2t / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NZD4
#2: Protein Iron-regulated surface determinant protein H / IsdH / Haptoglobin receptor A / Staphylococcus aureus surface protein I


Mass: 18904.824 Da / Num. of mol.: 1 / Fragment: first NEAT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MSSA476 / Gene: SAS1657 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6G8J7
#3: Protein Hemoglobin subunit alpha / / Hemoglobin alpha chain / Alpha-globin


Mass: 15150.353 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: blood / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.2 Å3/Da / Density % sol: 44.2 % / Description: The file contains Friedel pair. / Mosaicity: 1.401 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M sodium acetate, 20%(w/v) PEG 3350, 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: 1.74086, 1.73903, 1.67541
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 14, 2010
RadiationMonochromator: Double crystal (Si111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.740861
21.739031
31.675411
ReflectionRedundancy: 6.8 % / Av σ(I) over netI: 6.6 / Number: 128528 / Rmerge(I) obs: 0.177 / Χ2: 1.07 / D res high: 2.82 Å / D res low: 50 Å / Num. obs: 18921 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.822.8710010.8581.2345.7
2.872.9210010.6841.0866.2
2.922.9810010.6571.1246.7
2.983.0410010.5571.1386.7
3.043.110010.4921.0876.8
3.13.1810010.4051.0616.7
3.183.2610010.3631.0816.8
3.263.3410010.311.0926.8
3.343.4410010.2791.0676.8
3.443.5510010.2541.0816.9
3.553.6810010.2271.0617
3.683.8310010.2061.0597
3.83410010.1881.0787
44.2110010.1661.0057
4.214.4810010.1551.037
4.484.8210010.1381.0337
4.825.3110010.1351.0356.9
5.316.0710010.1311.0457
6.077.6510010.1151.0196.8
7.655010010.111.0457.3
ReflectionResolution: 2.83→50 Å / Num. all: 18538 / Num. obs: 18538 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.163 / Χ2: 1.034 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.83-2.882.90.6691.69331.10199.7
2.88-2.933.20.552.19171.09299.9
2.93-2.993.30.5392.19371.07899.6
2.99-3.053.30.4552.59131.06499.6
3.05-3.113.30.39239491.02899.4
3.11-3.193.40.3523.29051.02499.7
3.19-3.273.30.3093.69271.05299.8
3.27-3.363.30.2734.19161.03499.9
3.36-3.453.30.2514.49290.989100
3.45-3.573.40.2284.99451.06599.7
3.57-3.693.40.2075.59111.023100
3.69-3.843.40.1915.89130.99799.9
3.84-4.023.40.1726.79361.07699.8
4.02-4.233.40.1586.99301.00499.7
4.23-4.493.50.1487.29260.95399.8
4.49-4.843.50.1348.39321.09699.8
4.84-5.323.40.1318.19261.00599.8
5.32-6.093.40.138.49240.99699.8
6.09-7.673.40.11899331.02599.7
7.67-503.60.1198.89361.01100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.83→49.57 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.887 / WRfactor Rfree: 0.3026 / WRfactor Rwork: 0.2785 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7802 / SU B: 44.029 / SU ML: 0.395 / SU R Cruickshank DPI: 0.408 / SU Rfree: 0.4532 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The file contains Friedel pair. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2802 477 4.8 %RANDOM
Rwork0.2521 ---
all0.2534 ---
obs0.2534 18538 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.24 Å2 / Biso mean: 67.188 Å2 / Biso min: 4.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--2.03 Å20 Å2
3----2.52 Å2
Refinement stepCycle: LAST / Resolution: 2.83→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 0 43 3 2961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0223036
X-RAY DIFFRACTIONr_bond_other_d0.0010.021970
X-RAY DIFFRACTIONr_angle_refined_deg0.6571.9974143
X-RAY DIFFRACTIONr_angle_other_deg0.70234835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5145368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.76425.036137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.1115486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.071158
X-RAY DIFFRACTIONr_chiral_restr0.0380.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0213375
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02582
X-RAY DIFFRACTIONr_mcbond_it0.22921859
X-RAY DIFFRACTIONr_mcbond_other0.032732
X-RAY DIFFRACTIONr_mcangle_it0.4532992
X-RAY DIFFRACTIONr_scbond_it0.60341177
X-RAY DIFFRACTIONr_scangle_it1.00761151
LS refinement shellResolution: 2.825→2.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 22 -
Rwork0.323 601 -
all-623 -
obs--85.93 %
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)
18.3489-0.7982-6.22422.09840.835410.3490.53520.41080.75380.0560.12350.2185-1.0045-0.3583-0.65870.44340.00260.07610.19580.07350.4619-3.421935.77551.7587
21.42081.1401-0.18015.48380.51171.81220.07440.1374-0.09020.0428-0.01580.0730.2544-0.2373-0.05860.3770.0248-0.03150.3232-0.02410.2844-10.8457-3.621-4.214
34.2865-0.61341.03469.7635-0.26175.19070.07690.2088-0.2779-0.34430.0406-0.44910.15510.0924-0.11750.277-0.0204-0.03380.2715-0.04830.1785-6.6492-4.2018-7.317
4-0.0010.66641.07222.94173.2026.49120.1594-0.2502-0.12850.2520.0692-0.20870.09660.028-0.22860.3569-0.0517-0.01720.44650.02030.4167-0.942619.350816.6097
50.6621-0.17420.12283.24371.29984.58980.2544-0.22770.00090.2627-0.14280.15530.132-0.0675-0.11160.3348-0.05160.00140.3125-0.00260.3911-6.400316.443517.208
61.20312.3213-3.29822.3115-0.288712.24590.2386-0.13990.27820.4117-0.11840.2308-0.5359-0.4507-0.12020.375-0.0054-0.00220.3280.02990.399-11.195620.40849.9829
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 91
2X-RAY DIFFRACTION2B84 - 156
3X-RAY DIFFRACTION3B157 - 227
4X-RAY DIFFRACTION4C2 - 50
5X-RAY DIFFRACTION5C51 - 117
6X-RAY DIFFRACTION6C118 - 140

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