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- PDB-4ij2: Human methemoglobin in complex with the second and third NEAT dom... -

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Basic information

Entry
Database: PDB / ID: 4ij2
TitleHuman methemoglobin in complex with the second and third NEAT domains of IsdH from Staphylococcus aureus
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
  • Iron-regulated surface determinant protein H
KeywordsOXYGEN TRANSPORT/PROTEIN BINDING / NEAT / Heme/Hemoglobin binding / Hemoglobin / Cell wall associated / 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 / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / 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 / response to hydrogen peroxide / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / 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 / inflammatory response / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
Iron-regulated surface determinant protein H / : / Iron-regulated surface determinant protein H/B, linker domain / 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 / 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 / Globin / Globin / Globin domain profile. / Globin-like superfamily
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: 4.24 Å
AuthorsDickson, C.F. / 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
DepositionDec 21, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 8, 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_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_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_label_asym_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: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
E: Iron-regulated surface determinant protein H
F: Iron-regulated surface determinant protein H
G: Iron-regulated surface determinant protein H
H: Iron-regulated surface determinant protein H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,89612
Polymers217,4308
Non-polymers2,4664
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.903, 185.297, 103.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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) / Tissue: red blood cells / 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) / Tissue: red blood cells / References: UniProt: P68871
#3: Protein
Iron-regulated surface determinant protein H / Haptoglobin receptor A / Staphylococcus aureus surface protein I


Mass: 38837.305 Da / Num. of mol.: 4 / Fragment: NEAT2, NEAT3, UNP residues 326-660 / Mutation: Y642A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: USA300 / Gene: isdH / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)pLysS / References: UniProt: Q2FG07
#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: 57.91 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Mosaicity: 0.931 °
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M diammonium citrate, 13%(w/v) PEG3350, 0.7% 1-butanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2011
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 4.24→50 Å / Num. all: 34745 / Num. obs: 34745 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.092 / Χ2: 1.083 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
4.24-4.323.80.72717601.181100
4.32-4.43.80.66317081.2171100
4.4-4.493.80.62417261.1431100
4.49-4.583.80.57617591.131100
4.58-4.683.80.48317281.1181100
4.68-4.793.80.40317271.0951100
4.79-4.913.80.35617481.1611100
4.91-5.043.80.34117301.1141100
5.04-5.193.80.31317541.1151100
5.19-5.353.80.28817271.0541100
5.35-5.543.80.24617381.0361100
5.54-5.773.80.22617591.0641100
5.77-6.033.80.19817361.0631100
6.03-6.353.80.1717181.0591100
6.35-6.743.80.15617601.0411100
6.74-7.263.80.12817291.019199.9
7.26-7.993.80.10617471.0111100
7.99-9.143.70.08117300.9771100
9.14-11.493.70.06617511.0191100
11.49-503.80.05117101.033197.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.24 Å49.71 Å
Translation4.24 Å49.71 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
HKL-2000data reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P5Q, 2E7D, 4FC3, 2LHR

3p5q

2e7d

4fc3

2lhr


Resolution: 4.24→29.15 Å / Cor.coef. Fo:Fc: 0.6728 / Cor.coef. Fo:Fc free: 0.6675 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflectionSelection details
Rfree0.3102 945 5.11 %RANDOM
Rwork0.2995 ---
obs0.3001 18511 99.4 %-
all-18511 --
Displacement parametersBiso max: 300 Å2 / Biso mean: 86.1417 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--8.4334 Å20 Å20 Å2
2---5.82 Å20 Å2
3---14.2534 Å2
Refine analyzeLuzzati coordinate error obs: 1.555 Å
Refinement stepCycle: LAST / Resolution: 4.24→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13375 0 172 0 13547
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6339SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes351HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1959HARMONIC5
X-RAY DIFFRACTIONt_it13884HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1774SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14311SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13884HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg18875HARMONIC20.84
X-RAY DIFFRACTIONt_omega_torsion1.39
X-RAY DIFFRACTIONt_other_torsion3.15
LS refinement shellResolution: 4.24→4.5 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2786 142 4.96 %
Rwork0.2911 2720 -
all0.2905 2862 -
obs--99.4 %
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)
14.10370.5093-1.96716.81011.20148.31550.15080.54420.5442-0.5442-0.24580.4863-0.5442-0.54420.095-0.3040.1063-0.04440.304-0.152-0.304-51.253614.0018-26.2819
28.31550.3766-2.910402.91040-0.0403-0.2881-0.18680.54420.3579-0.5442-0.0890.4162-0.31760.05320.13070.0083-0.304-0.152-0.304-53.213115.0603-1.7414
38.3155-0.3017-2.91048.3155-2.12228.3155-0.039-0.54420.00280.5442-0.3126-0.30570.54420.54420.3517-0.3040.1520.1013-0.2985-0.0485-0.0596-24.966625.3146-11.8589
45.4119-0.2229-2.16448.31552.63463.30430.22360.54420.0266-0.5442-0.04150.5442-0.5442-0.5442-0.1821-0.29170.1520.152-0.06810.1520.304-42.095142.1777-15.6076
54.6206-2.9104-2.91046.8041-2.90546.95820.03960.19-0.4467-0.2371-0.19070.5442-0.5442-0.54420.15110.3040.1520.152-0.3040.027-0.0997-80.683823.14228.3301
60.41330.60440.66044.02090.49222.09510.1310.5442-0.0757-0.5442-0.13730.5442-0.4478-0.07370.0063-0.16410.1520.1520.3040.15140.0733-4.916124.5945-34.675
78.31550.1637-1.79514.77642.91048.07440.0048-0.1633-0.54420.2344-0.28240.41790.54420.54420.2776-0.13350.152-0.06130.304-0.152-0.2384-41.5101-12.6609-35.9033
85.6571-2.9104-0.58266.508-0.43733.4831-0.2863-0.54420.15420.45710.1939-0.54420.54420.36380.09240.27160.1520.152-0.304-0.02790.2661-43.722862.65736.7388
98.06970.78582.91047.314-2.91041.4544-0.0515-0.54420.50670.5442-0.13540.15990.268-0.09360.1868-0.06290.02990.152-0.1430.1520.304-4.811715.418413.3612
108.3155-1.96572.7911.3437-0.84648.31550.10260.484-0.06920.28430.3391-0.54420.15070.4549-0.44170.304-0.1520.1520.304-0.152-0.304-42.33050.123925.6623
110-2.9104-2.09241.1012-2.91040-0.05250.20240.33130.19220.1830.1466-0.25660.3869-0.1305-0.1934-0.1520.04970.017-0.152-0.304-39.020416.9655-52.5251
122.0779-1.7822-2.91041.112-2.91040-0.02560.1233-0.277-0.12290.1401-0.4871-0.47680.0247-0.11450.1134-0.1520.152-0.2623-0.152-0.304-50.345528.101625.0306
1302.9104-2.91041.6734-0.14596.47220.21670.54420.01470.0442-0.0470.1968-0.1374-0.0782-0.1698-0.1555-0.152-0.0577-0.3040.09840.304-10.11130.5724-10.9274
1402.91042.910402.91040-0.02970.4169-0.1941-0.47630.08730.09120.3286-0.3163-0.0575-0.3040.1520.0533-0.304-0.1520.304-68.864254.5961-15.712
152.7827-2.9104-2.12678.3155-2.78518.31550.0641-0.16730.54420.01290.2899-0.1273-0.497-0.3952-0.3540.304-0.1520.1520.304-0.152-0.304-67.196923.9574-53.2233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|139 }A1 - 139
2X-RAY DIFFRACTION2{ B|1 - B|146 }B1 - 146
3X-RAY DIFFRACTION3{ C|1 - C|139 }C1 - 139
4X-RAY DIFFRACTION4{ D|1 - D|146 }D1 - 146
5X-RAY DIFFRACTION5{ E|326 - E|464 }E326 - 464
6X-RAY DIFFRACTION6{ F|326 - F|464 }F326 - 464
7X-RAY DIFFRACTION7{ G|326 - G|464 }G326 - 464
8X-RAY DIFFRACTION8{ H|326 - H|464 }H326 - 464
9X-RAY DIFFRACTION9{ F|544 - F|655 }F544 - 655
10X-RAY DIFFRACTION10{ E|544 - E|655 }E544 - 655
11X-RAY DIFFRACTION11{ G|473 - G|530 }G473 - 530
12X-RAY DIFFRACTION12{ E|473 - E|530 }E473 - 530
13X-RAY DIFFRACTION13{ F|473 - F|530 }F473 - 530
14X-RAY DIFFRACTION14{ H|473 - H|530 }H473 - 530
15X-RAY DIFFRACTION15{ G|544 - G|655 }G544 - 655

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