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- PDB-1jeb: Chimeric Human/Mouse Carbonmonoxy Hemoglobin (Human Zeta2 / Mouse... -

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Basic information

Entry
Database: PDB / ID: 1jeb
TitleChimeric Human/Mouse Carbonmonoxy Hemoglobin (Human Zeta2 / Mouse Beta2)
Components
  • HEMOGLOBIN BETA-SINGLE CHAIN
  • HEMOGLOBIN ZETA CHAIN
KeywordsOXYGEN STORAGE/TRANSPORT / oxygen transport / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


nitric oxide transport / cellular oxidant detoxification / erythrocyte maturation / haptoglobin-hemoglobin complex / erythrocyte development / hemoglobin complex / oxygen transport / hemopoiesis / hydrogen peroxide catabolic process / oxygen carrier activity ...nitric oxide transport / cellular oxidant detoxification / erythrocyte maturation / haptoglobin-hemoglobin complex / erythrocyte development / hemoglobin complex / oxygen transport / hemopoiesis / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / oxygen binding / myelin sheath / iron ion binding / heme binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / metal ion binding
Similarity search - Function
Hemoglobin, zeta / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. ...Hemoglobin, zeta / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit zeta / Hemoglobin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKidd, R.D. / Russell, J.E. / Watmough, N.J. / Baker, E.N. / Brittain, T.
CitationJournal: Biochemistry / Year: 2001
Title: The role of beta chains in the control of the hemoglobin oxygen binding function: chimeric human/mouse proteins, structure, and function.
Authors: Kidd, R.D. / Russell, J.E. / Watmough, N.J. / Baker, E.N. / Brittain, T.
History
DepositionJun 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_conn_type / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMOGLOBIN ZETA CHAIN
B: HEMOGLOBIN BETA-SINGLE CHAIN
C: HEMOGLOBIN ZETA CHAIN
D: HEMOGLOBIN BETA-SINGLE CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,96512
Polymers62,3874
Non-polymers2,5788
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.921, 84.921, 104.523
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein HEMOGLOBIN ZETA CHAIN


Mass: 15553.847 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: transgenic-knockout mouse expressing chimeric human zeta / mouse beta-single hemoglobin
Gene: HBZ / Production host: Mus musculus (house mouse) / Strain (production host): BALB/c / References: UniProt: P02008
#2: Protein HEMOGLOBIN BETA-SINGLE CHAIN / B SINGLE


Mass: 15639.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: transgenic-knockout mouse expressing chimeric human zeta / mouse beta-single hemoglobin
Source: (natural) Mus musculus (house mouse) / References: UniProt: P02088
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
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: 2.92 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Bicine/NaOH, MePEG 550, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1drop
20.1 MHEPES1droppH7.4
32 mMsodium dithionite1drop
40.1 MBicine-NaOH1reservoirpH8.5
533 %MePEG5501reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2001 / Details: mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 43348 / Num. obs: 43348 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4307 / % possible all: 100
Reflection
*PLUS
Num. measured all: 192738
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BBB

1bbb


Resolution: 2.1→25 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 4162 10.1 %random
Rwork0.216 ---
all-41201 --
obs-41201 95.3 %-
Solvent computationSolvent model: flat model / Bsol: 39.5297 Å2 / ksol: 0.304517 e/Å3
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.04 Å20 Å20 Å2
2--4.04 Å20 Å2
3----8.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4374 0 180 234 4788
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d16.2
X-RAY DIFFRACTIONc_improper_angle_d1.08
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.395 671 10.5 %
Rwork0.379 5704 -
obs-5704 88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2HEM_XPLOR.PARHEM_XPLOR.TOP
X-RAY DIFFRACTION3CMO_XPLOR.PARCMO_XPLOR.TOP
X-RAY DIFFRACTION4ACE_XPLOR.PARACE_XPLOR.TOP
X-RAY DIFFRACTION5WATER_REP.PARAMWATER_REP.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 28 Å / Num. reflection obs: 43240 / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.08
LS refinement shell
*PLUS
Rfactor Rfree: 0.395 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.379

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