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- PDB-1kd2: Crystal Structure of Human Deoxyhemoglobin in Absence of Any Anions -

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Basic information

Entry
Database: PDB / ID: 1kd2
TitleCrystal Structure of Human Deoxyhemoglobin in Absence of Any Anions
Components
  • Hemoglobin alpha chain
  • Hemoglobin beta chain
KeywordsOXYGEN STORAGE/TRANSPORT / HUMAN DEOXY HEMOGLOBIN / HIGH O2 AFFINITY T STATE / CHLORIDE BINDING SITES / ALLOSTERIC ANION BINDING SITES / HYDRATION / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / 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 / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / regulation of blood pressure / 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 / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsColombo, M.F. / Seixas, F.A.V.
Citation
Journal: To be Published
Title: The X-Ray Structure of Iso-Ionic Deoxy-Hb Crystal: The High Affinity T-state of Human Hb and the Mechanism of Chloride Regulation of Hb Cooperative Oxygen Binding.
Authors: Seixas, F.A.V. / Azevedo Jr, W.F. / Colombo, M.F.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and X-ray Diffraction Data Analysis of Human Deoxyhaemoglobin A(0) Fully stripped of Any Anions
Authors: Seixas, F.A.V. / Azevedo Jr, W.F. / Colombo, M.F.
History
DepositionNov 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: 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_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_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_seq_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_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Hemoglobin alpha chain
B: Hemoglobin beta chain
C: Hemoglobin alpha chain
D: Hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5478
Polymers62,0814
Non-polymers2,4664
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11330 Å2
ΔGint-101 kcal/mol
Surface area23340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.339, 99.348, 66.123
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS TWO ALPHA AND TWO BETA CHAINS.

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Components

#1: Protein Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: BLOOD / References: UniProt: P69905
#2: Protein Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: BLOOD / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 298 K / Method: batch method / pH: 7
Details: DEIONIZED PEG 3350 12.5%, pH 7.0, BATCH METHOD, temperature 298K

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Data collection

DiffractionMean temperature: 299 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 26, 1998
RadiationMonochromator: SILICON CRYSTAL WITH ASYMMETRIC CUT. ASYMMETRIC ANGLE: 7.25 DEGREES, CONDENSATE MODE
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 1.87→69.007 Å / Num. all: 51413 / Num. obs: 51030 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.8 / Rsym value: 0.062
Reflection shellResolution: 1.87→1.91 Å / Num. unique all: 3240 / Rsym value: 0.348 / % possible all: 92.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
REFMACrefinement
XTALVIEWrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HHB

2hhb


Resolution: 1.87→10 Å / Isotropic thermal model: overall temperature factors / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 5124 RANDOM
Rwork0.198 --
all-51413 -
obs-51030 -
Displacement parametersBiso mean: 23.062 Å2
Refine analyzeLuzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.87→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 172 161 4717
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.613
X-RAY DIFFRACTIONx_dihedral_angle_d20.722
X-RAY DIFFRACTIONx_improper_angle_d1.648
LS refinement shellResolution: 1.87→1.91 Å
RfactorNum. reflection
Rfree0.25 5124
Rwork0.198 -
obs-51030

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