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- PDB-9ww1: Oxy-bound rHb0.1WT beta homotetramer human hemoglobin -

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Basic information

Entry
Database: PDB / ID: 9ww1
TitleOxy-bound rHb0.1WT beta homotetramer human hemoglobin
ComponentsHemoglobin subunit beta
KeywordsOXYGEN BINDING / beta homotetramer / human hemoglobin
Function / homology
Function and homology information


cellular oxidant detoxification / Heme assimilation / nitric oxide transport / hemoglobin alpha binding / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / hemoglobin complex / erythrocyte development / oxygen transport ...cellular oxidant detoxification / Heme assimilation / nitric oxide transport / hemoglobin alpha binding / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / hemoglobin complex / erythrocyte development / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / response to hydrogen peroxide / carbon dioxide transport / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / Late endosomal microautophagy / platelet aggregation / regulation of blood pressure / positive regulation of nitric oxide biosynthetic process / Chaperone Mediated Autophagy / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / inflammatory response / heme binding / Neutrophil degranulation / : / extracellular exosome / extracellular region / metal ion binding / cytosol
Similarity search - Function
Hemoglobin, beta-type / : / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Hemoglobin subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYadav, K. / Verma, S. / Kumar, P. / Kundu, S.
Funding support India, 1items
OrganizationGrant numberCountry
Other governmentDG(TM)/81/48222/LSRB-317/SH&DD/2017 India
CitationJournal: Acs Omega / Year: 2026
Title: Recombinant Hemoglobin rHb0.1 with Cross-Linked Alpha Subunits Preferentially Crystallizes in the beta 4 Oligomeric State, Potentially Driven by a beta G18(H116I) Mutation
Authors: Yadav, K. / Verma, S. / Nag, A. / Kumar, P. / Kundu, S.
History
DepositionSep 22, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _pdbx_entry_details.has_protein_modification / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit beta
B: Hemoglobin subunit beta
C: Hemoglobin subunit beta
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,54917
Polymers63,6454
Non-polymers2,90413
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13220 Å2
ΔGint-104 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.804, 80.947, 62.683
Angle α, β, γ (deg.)90, 90.399, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15911.300 Da / Num. of mol.: 4 / Mutation: V1M, G16A, H116I
Source method: isolated from a genetically manipulated source
Details: Oxy-bound rHb0.1WT beta homotetramer human hemoglobin
Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P68871
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.14442873 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion / pH: 8.8 / Details: 1.2 M Tri-sodium citrate pH 8.8, 15% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→27 Å / Num. obs: 36366 / % possible obs: 99.9 % / Redundancy: 4.02 % / CC1/2: 0.998 / Net I/σ(I): 16.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.76 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2650 / Rpim(I) all: 0.457 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ABW

1abw


Resolution: 2→22.497 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 11.191 / SU ML: 0.135 / Cross valid method: FREE R-VALUE / ESU R Free: 0.178 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2329 1817 4.999 %
Rwork0.1946 34529 -
all0.196 --
obs-36346 99.863 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.268 Å2
Baniso -1Baniso -2Baniso -3
1--0.105 Å2-0 Å2-0.313 Å2
2--0.302 Å2-0 Å2
3----0.193 Å2
Refinement stepCycle: LAST / Resolution: 2→22.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4492 0 200 125 4817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124882
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.8876687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6245594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.131512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14610745
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.90810194
X-RAY DIFFRACTIONr_chiral_restr0.130.2715
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023768
X-RAY DIFFRACTIONr_nbd_refined0.2270.22310
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23301
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2175
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3420.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2270.26
X-RAY DIFFRACTIONr_mcbond_it3.1851.7842367
X-RAY DIFFRACTIONr_mcangle_it5.0343.192964
X-RAY DIFFRACTIONr_scbond_it5.1562.1392515
X-RAY DIFFRACTIONr_scangle_it8.0423.7353723
X-RAY DIFFRACTIONr_lrange_it11.28221.117499
X-RAY DIFFRACTIONr_rigid_bond_restr7.76434882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.3131110.2692522X-RAY DIFFRACTION99.396
2.052-2.1070.2931390.252458X-RAY DIFFRACTION100
2.107-2.1680.2721580.2412371X-RAY DIFFRACTION100
2.168-2.2340.2541200.222331X-RAY DIFFRACTION100
2.234-2.3060.2521190.2172252X-RAY DIFFRACTION100
2.306-2.3860.2331000.1972186X-RAY DIFFRACTION100
2.386-2.4750.251090.1932108X-RAY DIFFRACTION100
2.475-2.5750.2561040.2152050X-RAY DIFFRACTION100
2.575-2.6880.2321400.2111929X-RAY DIFFRACTION100
2.688-2.8170.331810.1921876X-RAY DIFFRACTION100
2.817-2.9670.222800.191805X-RAY DIFFRACTION100
2.967-3.1440.211140.2011647X-RAY DIFFRACTION100
3.144-3.3560.238720.2051603X-RAY DIFFRACTION100
3.356-3.6180.24830.1881478X-RAY DIFFRACTION100
3.618-3.9530.225630.1791376X-RAY DIFFRACTION99.9306
3.953-4.4030.198700.1691238X-RAY DIFFRACTION100
4.403-5.0520.199400.1631125X-RAY DIFFRACTION100
5.052-6.1110.203500.174949X-RAY DIFFRACTION100
6.111-8.340.215340.173757X-RAY DIFFRACTION100
8-100.143300.126468X-RAY DIFFRACTION99.4012
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)
11.2158-0.2656-0.04621.3704-0.10011.0943-0.0861-0.05730.03630.0630.0639-0.1133-0.02230.11350.02220.0110.001-0.00580.0191-0.00480.009925.5956-0.025727.639
21.67-0.12450.35750.9505-0.36611.4771-0.0898-0.08430.06870.06430.08630.1833-0.1013-0.1150.00350.03340.02510.0230.02170.01960.05753.14597.769721.6311
30.8776-0.4351-0.38552.87940.04041.3130.12540.04950.1111-0.2382-0.0767-0.1124-0.08730.1401-0.04860.04930.00520.01150.07740.01570.020719.2861-1.7333-2.3351
41.4393-0.18610.41160.4291-0.02371.53490.1021-0.0049-0.1604-0.0071-0.05660.19950.2541-0.0498-0.04560.0764-0.0196-0.02870.0131-0.01790.106710.6278-20.306610.7046
Refinement TLS groupSelection: ALL

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