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- PDB-1hxn: 1.8 ANGSTROMS CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF RABBI... -

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Basic information

Entry
Database: PDB / ID: 1hxn
Title1.8 ANGSTROMS CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF RABBIT SERUM HEMOPEXIN
ComponentsHEMOPEXIN
KeywordsBINDING PROTEIN / HEME
Function / homology
Function and homology information


heme transmembrane transporter activity / intracellular iron ion homeostasis / heme binding / extracellular space / metal ion binding
Similarity search - Function
Hemopexin / : / 4 Propeller / Hemopexin / Hemopexin-like domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Hemopexin-like repeats / Hemopexin-like domain superfamily ...Hemopexin / : / 4 Propeller / Hemopexin / Hemopexin-like domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Hemopexin
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsFaber, H.R. / Baker, E.N.
Citation
Journal: Structure / Year: 1995
Title: 1.8 A crystal structure of the C-terminal domain of rabbit serum haemopexin.
Authors: Faber, H.R. / Groom, C.R. / Baker, H.M. / Morgan, W.T. / Smith, A. / Baker, E.N.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of the C-Terminal Domain of Rabbit Serum Hemopexin
Authors: Baker, H.M. / Norris, G.E. / Morgan, W.T. / Smith, A. / Baker, E.N.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: Identification of the Histidine Residues of Hemopexin that Coordinate with Heme-Iron and of a Receptor-Binding Region
Authors: Morgan, W.T. / Muster, P. / Tatum, F. / Kao, S.-M. / Alam, J. / Smith, A.
History
DepositionJun 1, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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.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_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.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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEMOPEXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8265
Polymers24,6501
Non-polymers1764
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.600, 62.800, 80.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 314

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Components

#1: Protein HEMOPEXIN / HPX


Mass: 24649.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: SERUM / References: UniProt: P20058
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsRESIDUES 2 AND 4 ARE PRESUMED TO BE SODIUM IONS BUT WOULD BE INDISTINGUISHABLE FROM MAGNESIUM IONS. ...RESIDUES 2 AND 4 ARE PRESUMED TO BE SODIUM IONS BUT WOULD BE INDISTINGUISHABLE FROM MAGNESIUM IONS. COMPARISON OF THERMAL PARAMETERS OF SURROUNDING ATOMS (INCLUDING THE CHLORIDE OF RESIDUE 3) RULES OUT THE POSSIBILITY OF CALCIUM IONS AT THESE SITES.
Sequence detailsTHE SEQUENCE IS GIVEN FOR THE C-TERMINAL PROTEOLYTIC FRAGMENT OF RABBIT SERUM HEMOPEXIN. THIS ...THE SEQUENCE IS GIVEN FOR THE C-TERMINAL PROTEOLYTIC FRAGMENT OF RABBIT SERUM HEMOPEXIN. THIS CONSISTS OF RESIDUES 215 - 434 OF THE INTACT MOLECULE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.25 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
20.1 Msodium citrate1drop
30.3 Mammonium acetate1drop
420 %(w/v)methoxypolyethylene glycol15001drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 16990 / % possible obs: 81 % / Observed criterion σ(I): 1.5 / Num. measured all: 51808 / Rmerge(I) obs: 0.04

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.8→20 Å / σ(F): 1 /
RfactorNum. reflection
obs0.176 16791
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 8 100 1738
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg1.2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 16971 / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS

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