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- PDB-1hv4: CRYSTAL STRUCTURE ANALYSIS OF BAR-HEAD GOOSE HEMOGLOBIN (DEOXY FORM) -

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Basic information

Entry
Database: PDB / ID: 1hv4
TitleCRYSTAL STRUCTURE ANALYSIS OF BAR-HEAD GOOSE HEMOGLOBIN (DEOXY FORM)
Components
  • HEMOGLOBIN ALPHA-A CHAIN
  • HEMOGLOBIN BETA CHAIN
KeywordsOXYGEN STORAGE/TRANSPORT / ALLOSTERIC MECHANISM / OXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding ...haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding / heme binding / 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-A / Hemoglobin subunit beta
Similarity search - Component
Biological speciesAnser indicus (Bar-headed goose)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLiang, Y. / Hua, Z. / Liang, X. / Xu, Q. / Lu, G.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The crystal structure of bar-headed goose hemoglobin in deoxy form: the allosteric mechanism of a hemoglobin species with high oxygen affinity.
Authors: Liang, Y. / Hua, Z. / Liang, X. / Xu, Q. / Lu, G.
History
DepositionJan 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 9, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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-A CHAIN
B: HEMOGLOBIN BETA CHAIN
C: HEMOGLOBIN ALPHA-A CHAIN
D: HEMOGLOBIN BETA CHAIN
E: HEMOGLOBIN ALPHA-A CHAIN
F: HEMOGLOBIN BETA CHAIN
G: HEMOGLOBIN ALPHA-A CHAIN
H: HEMOGLOBIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,63416
Polymers126,7028
Non-polymers4,9328
Water00
1
A: HEMOGLOBIN ALPHA-A CHAIN
B: HEMOGLOBIN BETA CHAIN
C: HEMOGLOBIN ALPHA-A CHAIN
D: HEMOGLOBIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8178
Polymers63,3514
Non-polymers2,4664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-111 kcal/mol
Surface area23400 Å2
MethodPISA
2
E: HEMOGLOBIN ALPHA-A CHAIN
F: HEMOGLOBIN BETA CHAIN
G: HEMOGLOBIN ALPHA-A CHAIN
H: HEMOGLOBIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8178
Polymers63,3514
Non-polymers2,4664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11360 Å2
ΔGint-111 kcal/mol
Surface area23370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.660, 94.100, 59.230
Angle α, β, γ (deg.)71.55, 65.10, 83.10
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
HEMOGLOBIN ALPHA-A CHAIN


Mass: 15361.679 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Anser indicus (Bar-headed goose) / Cell: ERYTHROCYTES / Cellular location: CYTOPLASM / Tissue: BLOOD / References: UniProt: P01990
#2: Protein
HEMOGLOBIN BETA CHAIN


Mass: 16313.866 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Anser indicus (Bar-headed goose) / Cell: ERYTHROCYTES / Cellular location: CYTOPLASM / Tissue: BLOOD / References: UniProt: P02118
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 6000, potassium phosphate , pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 mg/mlprotein1drop
25 %(w/v)PEG60001drop
330 %PEG60001reservoir
450 mMpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: SIEMENS X200 / Detector: AREA DETECTOR / Date: May 10, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.57→36.89 Å / Num. all: 45509 / Num. obs: 30654 / % possible obs: 67.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.1
Reflection shellResolution: 2.57→2.73 Å / Redundancy: 1.14 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1779 / % possible all: 24
Reflection
*PLUS
Num. measured all: 57884 / Rmerge(I) obs: 0.0541

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
IPCdata reduction
X-GENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A4F

1a4f


Resolution: 2.8→36.89 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 63263.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2752 10.1 %RANDOM
Rwork0.197 ---
all0.229 32306 --
obs0.197 27148 84 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.63 Å2 / ksol: 0.299 e/Å3
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å21.41 Å2-2.33 Å2
2---5.21 Å2-0.53 Å2
3---6.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.8→36.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8944 0 344 0 9288
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_improper_angle_d1.25
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 389 10.6 %
Rwork0.285 3268 -
obs-3657 68 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM19X.HEME-USETOPH19X.HEME-USE
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.25
LS refinement shell
*PLUS
Rfactor Rfree: 0.329 / % reflection Rfree: 10.6 % / Rfactor Rwork: 0.285

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