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- PDB-1abw: DEOXY RHB1.1 (RECOMBINANT HEMOGLOBIN) -

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Basic information

Entry
Database: PDB / ID: 1abw
TitleDEOXY RHB1.1 (RECOMBINANT HEMOGLOBIN)
Components(HEMOGLOBIN-BASED BLOOD ...) x 2
KeywordsOXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN / ERYTHROCYTE
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 / LEUCINE / METHIONINE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKundrot, C.E. / Kroeger, K.S.
Citation
Journal: Structure / Year: 1997
Title: Structures of a hemoglobin-based blood substitute: insights into the function of allosteric proteins.
Authors: Kroeger, K.S. / Kundrot, C.E.
#1: Journal: Nature / Year: 1992
Title: A Human Recombinant Haemoglobin Designed for Use as a Blood Substitute
Authors: Looker, D. / Abbott-Brown, D. / Cozart, P. / Durfee, S. / Hoffman, S. / Mathews, A.J. / Miller-Roehrich, J. / Shoemaker, S. / Trimble, S. / Fermi, G. / Komiyama, N.H. / Nagai, K. / Stetler, G.L.
History
DepositionJan 29, 1997Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 7 A NOTE FROM THE AUTHOR: RESIDUES 1001-1002 and 2001-2002 MODEL LOW OCCUPANCY STRUCTURES THAT HAVE ... A NOTE FROM THE AUTHOR: RESIDUES 1001-1002 and 2001-2002 MODEL LOW OCCUPANCY STRUCTURES THAT HAVE THEIR AMINO TERMINUS IN REGISTER WITH VAL A143. THE SPATIAL ARRANGEMENT OF TWO ALPHA CHAINS OF NORMAL HEMOGLOBIN CAN BE REPRESENTED SCHEMATICALLY AS GHIJ F A EDCB WHERE FGHIJ IS ONE COVALENT CHAIN AND ABCDE THE OTHER COVALENT CHAIN. IN THIS MUTANT HEMOGLOBIN, THERE IS A COVALENT BOND BETWEEN RESIDUE J AND A, BUT NOT BETWEEN E AND F. IN THE CRYSTAL, THE AUTHORS COULD HAVE GHIJ BCDE F A OR A F EDCB JIHG (1) (2) THE "F-A" CONTACT WOULD BE LIKE NORMAL HEMOGLOBIN, BUT THE "E-F" CONTACT HAS A COVALENT LINKAGE THAT BREAKS THE SYMMETRY. THE ONLY WAY TO TELL IF THE CRYSTAL STRUCTURE IS (1) OR (2) OR A MIXTURE OF THE TWO IS TO LOOK AT THE "E-F" AND "J-A" REGIONS. IN THIS STRUCTURE, IT COULD BE MOSTLY (1), BUT ABOUT 20% OF THE MOLECULES MAY BE FLIPPED OVER LIKE (2). THAT FLIPPING WOULD PUT THE N-TERMINAL METHIONINE ON TOP OF VAL 143. THUS, THE ELECTRON DENSITY MAP AT POSITION VAL 143 IS MOSTLY FROM VAL 143, BUT IT ALSO CONTAINS A LITTLE ELECTRON DENSITY FROM MET 1 FROM FLIPPED MOLECULES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMOGLOBIN-BASED BLOOD SUBSTITUTE
B: HEMOGLOBIN-BASED BLOOD SUBSTITUTE
D: HEMOGLOBIN-BASED BLOOD SUBSTITUTE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,27311
Polymers62,2473
Non-polymers3,0278
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-111 kcal/mol
Surface area23440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.900, 81.980, 53.920
Angle α, β, γ (deg.)90.00, 98.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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HEMOGLOBIN-BASED BLOOD ... , 2 types, 3 molecules ABD

#1: Protein HEMOGLOBIN-BASED BLOOD SUBSTITUTE


Mass: 30371.846 Da / Num. of mol.: 1
Mutation: CHAIN A IS COMPOSED OF TWO COPIES OF HEMOGLOBIN ALPHA CHAIN JOINED BY AN ADDITIONAL RESIDUE, GLY 142
Source method: isolated from a genetically manipulated source
Details: HUMAN HEMOGLOBIN HAS TWO ALPHA CHAINS WHICH ARE CALLED CHAINS A AND C IN OTHER PDB FILES. IN THIS ENTRY THE TWO ALPHA CHAINS HAVE BEEN COVALENTLY JOINED TOGETHER BY ONE GLYCINE RESIDUE TO ...Details: HUMAN HEMOGLOBIN HAS TWO ALPHA CHAINS WHICH ARE CALLED CHAINS A AND C IN OTHER PDB FILES. IN THIS ENTRY THE TWO ALPHA CHAINS HAVE BEEN COVALENTLY JOINED TOGETHER BY ONE GLYCINE RESIDUE TO FORM ONE COVALENTLY LINKED POLYPEPTIDE CHAIN.
Source: (gene. exp.) Homo sapiens (human) / Organ: BLOOD / Production host: Escherichia coli (E. coli) / References: UniProt: P69905
#2: Protein HEMOGLOBIN-BASED BLOOD SUBSTITUTE


Mass: 15937.343 Da / Num. of mol.: 2
Mutation: CHAIN A IS COMPOSED OF TWO COPIES OF HEMOGLOBIN ALPHA CHAIN JOINED BY AN ADDITIONAL RESIDUE, GLY 142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: BLOOD / Production host: Escherichia coli (E. coli) / References: UniProt: P68871

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Non-polymers , 4 types, 381 molecules

#3: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsHUMAN HEMOGLOBIN HAS TWO ALPHA CHAINS WHICH ARE CALLED CHAINS A AND C IN OTHER PDB FILES. IN THIS ...HUMAN HEMOGLOBIN HAS TWO ALPHA CHAINS WHICH ARE CALLED CHAINS A AND C IN OTHER PDB FILES. IN THIS ENTRY THE TWO ALPHA CHAINS HAVE BEEN COVALENTLY JOINED TOGETHER BY ONE GLYCINE RESIDUE TO FORM ONE COVALENTLY LINKED POLYPEPTIDE CHAIN.
Nonpolymer detailsTHE RESIDUES 1001-1002 AND 2001-2002 REPRESENT LOW OCCUPANCY DIPEPTIDES (MET-LEU) THAT HAVE THEIR ...THE RESIDUES 1001-1002 AND 2001-2002 REPRESENT LOW OCCUPANCY DIPEPTIDES (MET-LEU) THAT HAVE THEIR AMINO TERMINUS IN REGISTER WITH VAL A143
Sequence detailsGLY A 142 COVALENTLY LINKS HUMAN ALPHA CHAIN A AND C

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growpH: 6.2 / Details: pH 6.2
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
26.5 %PEG33501drop
375 mMammonium acetate1drop
40.25 mMKCN1drop
513 %PEG33501reservoir
6150 mMammonium acetate1reservoir
710 mMKCN1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 1, 1993 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→82 Å / Num. obs: 34054 / % possible obs: 77.1 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.046
Reflection shellResolution: 2→2.2 Å / % possible all: 56.1
Reflection
*PLUS
Num. measured all: 70840
Reflection shell
*PLUS
% possible obs: 56.1 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HHB

2hhb


Resolution: 2→5 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
Details: A NOTE FROM THE AUTHOR: CHAINS L AND P MODEL LOW OCCUPANCY STRUCTURES THAT HAVE THEIR AMINO TERMINUS IN REGISTER WITH VAL A143. THE SPATIAL ARRANGEMENT OF TWO ALPHA CHAINS OF NORMAL ...Details: A NOTE FROM THE AUTHOR: CHAINS L AND P MODEL LOW OCCUPANCY STRUCTURES THAT HAVE THEIR AMINO TERMINUS IN REGISTER WITH VAL A143. THE SPATIAL ARRANGEMENT OF TWO ALPHA CHAINS OF NORMAL HEMOGLOBIN CAN BE REPRESENTED SCHEMATICALLY AS GHIJ F A EDCB WHERE FGHIJ IS ONE COVALENT CHAIN AND ABCDE THE OTHER COVALENT CHAIN. IN THIS MUTANT HEMOGLOBIN, THERE IS A COVALENT BOND BETWEEN RESIDUE J AND A, BUT NOT BETWEEN E AND F. IN THE CRYSTAL, THE AUTHORS COULD HAVE GHIJ BCDE F A OR A F EDCB JIHG (1) (2) THE "F-A" CONTACT WOULD BE LIKE NORMAL HEMOGLOBIN, BUT THE "E-F" CONTACT HAS A COVALENT LINKAGE THAT BREAKS THE SYMMETRY. THE ONLY WAY TO TELL IF THE CRYSTAL STRUCTURE IS (1) OR (2) OR A MIXTURE OF THE TWO IS TO LOOK AT THE "E-F" AND "J-A" REGIONS. IN THIS STRUCTURE, IT COULD BE MOSTLY (1), BUT ABOUT 20% OF THE MOLECULES MAY BE FLIPPED OVER LIKE (2). THAT FLIPPING WOULD PUT THE N-TERMINAL METHIONINE ON TOP OF VAL 143. THUS, THE ELECTRON DENSITY MAP AT POSITION VAL 143 IS MOSTLY FROM VAL 143, BUT IT ALSO CONTAINS A LITTLE ELECTRON DENSITY FROM MET 1 FROM FLIPPED MOLECULES.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3141 10 %RANDOM
Rwork0.164 ---
obs0.164 31528 86.2 %-
Displacement parametersBiso mean: 13.3 Å2
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4392 0 206 373 4971
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.09
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it10
X-RAY DIFFRACTIONx_mcangle_it10
X-RAY DIFFRACTIONx_scbond_it10
X-RAY DIFFRACTIONx_scangle_it10
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.266 337 0.746 %
Rwork0.213 2972 -
obs--73.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARHCSDX.HEMETOPHCSDX.HEME
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.09
LS refinement shell
*PLUS
Rfactor obs: 0.213

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