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- PDB-9iux: X-ray crystal structure of human hemoglobin subunit mu C49S/C104S... -

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Basic information

Entry
Database: PDB / ID: 9iux
TitleX-ray crystal structure of human hemoglobin subunit mu C49S/C104S mutant
ComponentsHemoglobin subunit mu
KeywordsMETAL BINDING PROTEIN / hemoglobin
Function / homology
Function and homology information


cellular oxidant detoxification / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, alpha-type / : / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsLin, Y.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: X-ray crystal structure of human hemoglobin subunit mu C49S/C104S mutant
Authors: Lin, Y.W.
History
DepositionJul 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit mu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2342
Polymers15,6181
Non-polymers6161
Water2,594144
1
A: Hemoglobin subunit mu
hetero molecules

A: Hemoglobin subunit mu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4694
Polymers31,2362
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1480 Å2
ΔGint-10 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.630, 40.630, 167.429
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-394-

HOH

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Components

#1: Protein Hemoglobin subunit mu / Hemoglobin mu chain / Mu-globin


Mass: 15617.913 Da / Num. of mol.: 1 / Mutation: C49S,C104S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBM, HBAP2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6B0K9
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: sodium acetate, sodium cacodylate, PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.47→41.86 Å / Num. obs: 24796 / % possible obs: 99.7 % / Redundancy: 15.5 % / Biso Wilson estimate: 14.62 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.043 / Rrim(I) all: 0.168 / Net I/σ(I): 13
Reflection shellResolution: 1.47→1.55 Å / Rmerge(I) obs: 2.479 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3492 / CC1/2: 0.52 / Rpim(I) all: 0.749 / Rrim(I) all: 2.597 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→32.85 Å / SU ML: 0.1454 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.7686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2013 1062 4.79 %
Rwork0.1729 21090 -
obs0.1742 22152 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.48 Å2
Refinement stepCycle: LAST / Resolution: 1.53→32.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1066 0 43 144 1253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00671200
X-RAY DIFFRACTIONf_angle_d0.93291660
X-RAY DIFFRACTIONf_chiral_restr0.0492184
X-RAY DIFFRACTIONf_plane_restr0.0099211
X-RAY DIFFRACTIONf_dihedral_angle_d10.1055167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.60.26721460.20942544X-RAY DIFFRACTION99.01
1.6-1.680.23771350.19042547X-RAY DIFFRACTION99.04
1.68-1.790.23521400.17852555X-RAY DIFFRACTION99.41
1.79-1.930.18631250.17362608X-RAY DIFFRACTION99.45
1.93-2.120.20811350.15732602X-RAY DIFFRACTION99.85
2.12-2.430.17261260.16262651X-RAY DIFFRACTION99.93
2.43-3.060.22581160.17862695X-RAY DIFFRACTION99.72
3.06-32.850.18261390.17012888X-RAY DIFFRACTION99.93
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)
10.137354734283-0.0747979159250.06552063847180.1989491092-0.04700907900250.1865925504770.0436896772549-0.03205824238990.00662179080713-0.0163988234163-0.07529839419720.01452014168810.0213380933840.0501253366866-0.0194914241320.105476447876-0.003791034747140.017995540450.1048406506210.002214185371980.10874947454610.12411595161.42445078197-9.20219700996
20.0700476857213-0.134635509436-0.08306142740870.1946809159120.1149705986030.149370996250.0278587066824-0.08988903979760.2212452236150.01926642811610.03390102189790.129159404210.06011247816560.1979052875090.01032430819220.0971551824181-0.00963751721983-0.004629263044930.1133403690440.0006025138553940.12092027142214.7314887062-1.40201958273-2.89290491979
30.2627383498990.0866374201685-0.2455057123440.1989012944230.04769318817160.200927220824-0.04983849744080.00718019302336-0.05631608973240.09663330682630.07133296677460.03742421972090.104994318442-0.05037376950480.03988475502570.1412117256850.01092606649480.003541201336130.106883121068-0.01920170463540.09847574936876.24863391862-6.37873220925-6.62670050268
40.124552432220.0152246101776-0.02552637770810.0154088587635-0.03224473404050.0318274384399-0.0319601337114-0.1657487368680.0381174659788-0.03186122483250.01151750880540.176482998760.0276120433806-0.114394219921-0.03223961449160.129643291923-0.007043382755630.01879464767260.1379320810430.04086970770130.1535662268984.203699856019.14647753593-18.3030778012
50.2168561537660.117024202192-0.1463173617190.341162093788-0.2495647628060.394645280909-0.07952279626840.0552134566288-0.04898754089040.00485920919138-0.061083903474-0.05245544276720.05846108267570.0317288861973-0.1199244264750.1019376953120.01083781519820.002632059796470.118849543272-0.01493895931810.11720003727812.9580882826-6.27132102557-14.4369853376
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 80 through 116 )80 - 11676 - 112
22chain 'A' and (resid 117 through 141 )117 - 141113 - 137
33chain 'A' and (resid 1 through 35 )1 - 351 - 35
44chain 'A' and (resid 36 through 52 )36 - 5236 - 48
55chain 'A' and (resid 53 through 79 )53 - 7949 - 75

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