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- PDB-1a9w: HUMAN EMBRYONIC GOWER II CARBONMONOXY HEMOGLOBIN -

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Basic information

Entry
Database: PDB / ID: 1a9w
TitleHUMAN EMBRYONIC GOWER II CARBONMONOXY HEMOGLOBIN
Components
  • HEMOGLOBIN (ALPHA CHAIN)
  • HEMOGLOBIN (BETA CHAIN)
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / hydrogen peroxide catabolic process ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / hydrogen peroxide catabolic process / oxygen carrier activity / 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 / response to organic cyclic compound / oxygen binding / blood coagulation / Factors involved in megakaryocyte development and platelet production / blood microparticle / iron ion binding / heme binding / protein-containing complex binding / 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit epsilon / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSutherland-Smith, A.J. / Baker, H.M. / Hofmann, O.M. / Brittain, T. / Baker, E.N.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of a human embryonic haemoglobin: the carbonmonoxy form of gower II (alpha2 epsilon2) haemoglobin at 2.9 A resolution.
Authors: Sutherland-Smith, A.J. / Baker, H.M. / Hofmann, O.M. / Brittain, T. / Baker, E.N.
History
DepositionApr 11, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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: HEMOGLOBIN (ALPHA CHAIN)
E: HEMOGLOBIN (BETA CHAIN)
C: HEMOGLOBIN (ALPHA CHAIN)
F: HEMOGLOBIN (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,06812
Polymers62,4904
Non-polymers2,5788
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11560 Å2
ΔGint-119 kcal/mol
Surface area23350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.800, 62.800, 320.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.24491, -0.87348, -0.42078), (-0.87586, 0.0132, 0.48238), (-0.41579, 0.48669, -0.76828)64.31423, 8.04574, 99.26502
2given(-0.2293, -0.87966, -0.41667), (-0.89043, 0.01667, 0.45481), (-0.39313, 0.47531, -0.7871)63.93441, 9.52063, 100.20728

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Components

#1: Protein HEMOGLOBIN (ALPHA CHAIN)


Mass: 15150.353 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HUMAN GOWER II EMBRYONIC HEMOGLOBIN / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PRMAE389 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): GSY112 / References: UniProt: P69905
#2: Protein HEMOGLOBIN (BETA CHAIN)


Mass: 16094.614 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HUMAN GOWER II EMBRYONIC HEMOGLOBIN / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PRMAE389 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): GSY112 / References: UniProt: P02100
#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: Chemical
ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO

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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: 2.47 Å3/Da / Density % sol: 51 %
Crystal growMethod: microseeding, macroseeding used to increase crystal size
pH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 21% MME-PEG 5000, 0.2M TAPS/ KOH, PH 8.5, 2MM DITHIONITE. THEN MICROSEEDING AND MACROSEEDING USED TO INCREASE CRYSTAL SIZE, microseeding and macroseeding used ...Details: PROTEIN WAS CRYSTALLIZED FROM 21% MME-PEG 5000, 0.2M TAPS/ KOH, PH 8.5, 2MM DITHIONITE. THEN MICROSEEDING AND MACROSEEDING USED TO INCREASE CRYSTAL SIZE, microseeding and macroseeding used to increase crystal size
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
20.01 MHEPES1drop
32 mMdithionite1drop
40.2 MTAPS-KOH1reservoir
521 %(w/v)MME PEG50001reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 1, 1994 / Details: 0.3 MM COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 14645 / % possible obs: 95.9 % / Observed criterion σ(I): 1.9 / Redundancy: 5.9 % / Biso Wilson estimate: 61.7 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 7.1
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.37 / % possible all: 76.3
Reflection
*PLUS
Num. obs: 14597 / Num. measured all: 118919
Reflection shell
*PLUS
% possible obs: 72.6 % / Rmerge(I) obs: 0.417

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Processing

Software
NameVersionClassification
AMoREphasing
TFFCmodel building
X-PLOR3.851refinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TFFCphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BBB

1bbb


Resolution: 2.9→40 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001
Isotropic thermal model: ONE B FOR MAIN CHAIN ATOM B FOR SIDE CHAIN ATOMS
Cross valid method: THROUGHOUT / σ(F): 0 / Details: TNT-5E ALSO USED
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1485 10.2 %RANDOM
Rwork0.185 ---
obs0.185 14598 95.9 %-
Displacement parametersBiso mean: 50.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2---1.2 Å20 Å2
3---2.83 Å2
Refine analyzeLuzzati sigma a obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4234 0 180 0 4414
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11RESTRAINTSX-RAY DIFFRACTION0.0151000
22X-RAY DIFFRACTION0.0481000
LS refinement shellResolution: 2.9→3.03 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.354 137 10 %
Rwork0.294 1232 -
obs--76.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2HEM.PROHEM.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.186 / Rfactor Rfree: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1
LS refinement shell
*PLUS
Lowest resolution: 2.97 Å / Rfactor Rfree: 0.366 / Rfactor obs: 0.301

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