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- PDB-1hbr: R-STATE FORM OF CHICKEN HEMOGLOBIN D -

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Basic information

Entry
Database: PDB / ID: 1hbr
TitleR-STATE FORM OF CHICKEN HEMOGLOBIN D
Components(PROTEIN (HEMOGLOBIN D)) x 2
KeywordsOXYGEN STORAGE/TRANSPORT / HEMOGLOBIN D (R-STATE) 1 / HEMOGLOBIN / AVIAN / HIGH COOPERATIITY / OXYGEN TRANSPORT / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Scavenging of heme from plasma / Cytoprotection by HMOX1 / Heme signaling / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / hemoglobin complex / Neutrophil degranulation ...Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Scavenging of heme from plasma / Cytoprotection by HMOX1 / Heme signaling / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / hemoglobin complex / Neutrophil degranulation / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / extracellular space / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. ...Hemoglobin, pi / 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
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha-D / Hemoglobin subunit beta
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKnapp, E. / Oliveira, M.A. / Xie, Q. / Ernst, S.R. / Riggs, A.F. / Hackert, M.L.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: The structural and functional analysis of the hemoglobin D component from chicken.
Authors: Knapp, J.E. / Oliveira, M.A. / Xie, Q. / Ernst, S.R. / Riggs, A.F. / Hackert, M.L.
#1: Journal: J.Mol.Biol. / Year: 1983
Title: Structure of Human Oxyhaemoglobin at 2.1 A Resolution
Authors: Shaanan, B.
#2: Journal: J.Biol.Chem. / Year: 1983
Title: The Nucleotide Sequence of the Adult Chicken Alpha-Globin Genes
Authors: Dodgson, J.B. / Engel, J.D.
#3: Journal: J.Biol.Chem. / Year: 1983
Title: Analysis of the Adult Chicken Beta-Globin Gene
Authors: Dolan, M. / Dodgson, J.B. / Engel, J.D.
History
DepositionDec 6, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software / Item: _software.name
Revision 1.4Aug 9, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / struct_conn / 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.pdbx_dist_value / _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_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: PROTEIN (HEMOGLOBIN D)
B: PROTEIN (HEMOGLOBIN D)
C: PROTEIN (HEMOGLOBIN D)
D: PROTEIN (HEMOGLOBIN D)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6148
Polymers64,1484
Non-polymers2,4664
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.960, 80.510, 82.110
Angle α, β, γ (deg.)90.00, 104.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.883125, -0.046056, 0.466871), (-0.046909, -0.998851, -0.009803), (0.466786, -0.013243, -0.884271)
Vector: -6.741, 1.13, 27.204)

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Components

#1: Protein PROTEIN (HEMOGLOBIN D) / HB D


Mass: 15715.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cell: ERYTHROCYTES / Cellular location: CYTOPLASM / Tissue: BLOOD / References: UniProt: P02001
#2: Protein PROTEIN (HEMOGLOBIN D) / HB D


Mass: 16357.919 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cell: ERYTHROCYTES / Cellular location: CYTOPLASM / Tissue: BLOOD / References: UniProt: P02112
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-30 %PEG335011
210-30 mMsalt11
320 mg/mlprotein12
450 mMTris-HCl12

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Mar 1, 1994 / Details: NO MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. obs: 29702 / % possible obs: 99.1 % / Redundancy: 9.6 % / Biso Wilson estimate: 28 Å2 / Rsym value: 8.1 / Net I/σ(I): 15.5
Reflection shellResolution: 2.3→2.5 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.3 / Rsym value: 23.9 / % possible all: 97.7
Reflection
*PLUS
Redundancy: 6.8 % / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
Rmerge(I) obs: 0.239

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
UCSD-systemdata reduction
UCSD-systemdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HHO

1hho


Resolution: 2.3→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2949 9.9 %RANDOM
Rwork0.222 ---
obs-29702 99.1 %-
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4331 0 172 147 4650
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.59
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it10.791.5
X-RAY DIFFRACTIONx_mcangle_it13.122
X-RAY DIFFRACTIONx_scbond_it12.12
X-RAY DIFFRACTIONx_scangle_it14.292.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 476 9.9 %
Rwork0.292 4343 -
obs--96.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19X.HEME2TOPH19X.HEME
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.59

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