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- PDB-1qjs: mammalian blood serum haemopexin glycosylated-native protein and ... -

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Basic information

Entry
Database: PDB / ID: 1qjs
Titlemammalian blood serum haemopexin glycosylated-native protein and in complex with its ligand haem
ComponentsHEMOPEXIN
KeywordsTRANSPORT PROTEIN / HAEM BINDING PROTEIN / BETA PROPELLER / HAEM BINDING AND TRANSPORT / IRON METABOLISM
Function / homology
Function and homology information


heme transmembrane transporter activity / intracellular iron ion homeostasis / heme binding / extracellular region / 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 ...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
PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Hemopexin
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SIR / Resolution: 2.9 Å
AuthorsPaoli, M. / Baker, H.M. / Morgan, W.T. / Smith, A. / Baker, E.N.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Crystal Structure of Hemopexin Reveals a Novel High-Affinity Heme Site Formed between Two Beta-Propeller Domains.
Authors: Paoli, M. / Anderson, B.F. / Baker, H.M. / Morgan, W.T. / Smith, A. / Baker, E.N.
History
DepositionJul 1, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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: HEMOPEXIN
B: HEMOPEXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,41318
Polymers103,6652
Non-polymers1,74916
Water0
1
A: HEMOPEXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7079
Polymers51,8321
Non-polymers8748
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HEMOPEXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7079
Polymers51,8321
Non-polymers8748
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.900, 69.900, 151.810
Angle α, β, γ (deg.)90.00, 108.16, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.43434, -0.90066, 0.01304), (-0.9007, -0.43411, 0.01709), (-0.00973, -0.01917, -0.99977)
Vector: 36.94379, -0.02645, 74.34145)

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Components

#1: Protein HEMOPEXIN /


Mass: 51832.293 Da / Num. of mol.: 2 / Fragment: BETA-PROPELLER DOMAIN, HAEM LIGAND / Source method: isolated from a natural source
Details: COVALENT LINK BETWEEN FE OF HAEM LIGAND AND (I) NE2 OF HIS 213 AND (II) NE2 OF HIS 266
Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: BLOOD SERUM / References: UniProt: P20058
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
Compound detailsTHIS ENTRY ACCOMPANIES PDB ENTRY 1QHU, WHICH IS FOR DEGLYCOSYLATED HAEMOPEXIN. THE CRYSTALS WERE ...THIS ENTRY ACCOMPANIES PDB ENTRY 1QHU, WHICH IS FOR DEGLYCOSYLATED HAEMOPEXIN. THE CRYSTALS WERE PREPARED WITH THE WILD TYPE PROTEIN IN ITS NATIVE GLYCOSYLATED STATE.
Sequence detailsTHE N-TERMINUS (-25 TO 24 IN PDB NUMBERING, 1 TO 48 IN SWS) IS DISORDERED IN THE ELECTRON DENSITY ...THE N-TERMINUS (-25 TO 24 IN PDB NUMBERING, 1 TO 48 IN SWS) IS DISORDERED IN THE ELECTRON DENSITY MAPS. THE NUMERING OF RESIDUES IS SUCH THAT IT IS CONSISTENT WITH THE RESIDUE NUMERING IN PDB ENTRY 1HXN FOR THE C-TERMINAL DOMAIN STRUCTURE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: HANGING DROP, 4 DEGREES CENTIGRADE. RESEVOIR SOLUTION: 15-22% PEG 6000, 0.1-0.2 M TRIS HCL PH 7.9, 0.05-0.1 M EDTA, 0.05-0.2 NACL, PROTEIN COMPLEX SOLUTION: 65 MG/ML IN 0.01 M TRIS PH 7.9, 0. ...Details: HANGING DROP, 4 DEGREES CENTIGRADE. RESEVOIR SOLUTION: 15-22% PEG 6000, 0.1-0.2 M TRIS HCL PH 7.9, 0.05-0.1 M EDTA, 0.05-0.2 NACL, PROTEIN COMPLEX SOLUTION: 65 MG/ML IN 0.01 M TRIS PH 7.9, 0.01 M NACL, 0.1 M EDTA
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
165 mg/mlprotein1drop
20.01 MTris-HCl1drop
30.01 MEDTA1drop
40.01 M1dropNaCl
515-22 %(w/v)PEG60001reservoir
60.1-0.2 MTris-HCl1reservoir
70.05-0.1 MEDTA1reservoir
80.05-0.2 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jun 15, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 20915 / % possible obs: 97.5 % / Redundancy: 2.2 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 6.2
Reflection shellResolution: 2.9→3.05 Å / Redundancy: 2 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.2 / % possible all: 87.5
Reflection shell
*PLUS
% possible obs: 87.5 %

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Processing

Software
NameClassification
DENZOdata reduction
Agrovatadata scaling
ROTAVATAdata scaling
AMoREphasing
MAMAphasing
REFMACrefinement
RefinementMethod to determine structure: SIR
Starting model: 1HXN AND 1FBL

1hxn

1fbl


Resolution: 2.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 2.5
Details: ELECTRON DENSITY FOR RESIDUES ARG 214, SER 215, HIS 223 AND C-TERMINAL HIS 435 IS POORLY DEFINED. FOR BOTH CHAINS A AND B RESIDUES 219 - 222 COULD NOT BE FITTED INTO THE ELECTRON DENSITY ...Details: ELECTRON DENSITY FOR RESIDUES ARG 214, SER 215, HIS 223 AND C-TERMINAL HIS 435 IS POORLY DEFINED. FOR BOTH CHAINS A AND B RESIDUES 219 - 222 COULD NOT BE FITTED INTO THE ELECTRON DENSITY MAPS AND ARE NOT INCLUDED IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.312 101 5 %RANDOM
Rwork0.255 ---
obs0.251 20915 97.5 %-
Displacement parametersBiso mean: 39 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6578 0 108 0 6686
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0410.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1930.3
X-RAY DIFFRACTIONp_multtor_nbd0.2350.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor15.120
X-RAY DIFFRACTIONp_staggered_tor23.530
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.550
X-RAY DIFFRACTIONp_special_tor

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