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- PDB-1qhu: MAMMALIAN BLOOD SERUM HAEMOPEXIN DEGLYCOSYLATED AND IN COMPLEX WI... -

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Basic information

Entry
Database: PDB / ID: 1qhu
TitleMAMMALIAN BLOOD SERUM HAEMOPEXIN DEGLYCOSYLATED AND IN COMPLEX WITH ITS LIGAND HAEM
ComponentsPROTEIN (HEMOPEXIN)
KeywordsBINDING 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 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
PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Hemopexin
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionMay 27, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Oct 6, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 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: PROTEIN (HEMOPEXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7079
Polymers51,8321
Non-polymers8748
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.680, 61.950, 83.290
Angle α, β, γ (deg.)90.00, 93.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PROTEIN (HEMOPEXIN)


Mass: 51832.293 Da / Num. of mol.: 1 / Fragment: BETA-PROPELLER DOMAIN / 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 265
Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: BLOOD SERUM / References: UniProt: P20058

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Non-polymers , 5 types, 218 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsPROTEIN WAS DEGLYSOSYLATED PRIOR TO CRYSTALLISATION
Has protein modificationY
Nonpolymer detailsLIGAND COMPLEXED TO HAEMOPEXIN ION BOUND IN THE CENTRAL TUNNEL OF THE C-TERMINAL DOMAIN IONS BOUND ...LIGAND COMPLEXED TO HAEMOPEXIN ION BOUND IN THE CENTRAL TUNNEL OF THE C-TERMINAL DOMAIN IONS BOUND IN THE CENTRAL TUNNEL ION BOUND IN THE CENTRAL TUNNEL
Sequence detailsN-TERMINUS IS DISORDERED IN ELECTRON DENSITY MAPS NUMERING OF RESIDUES IS SUCH THAT IT IS ...N-TERMINUS IS DISORDERED IN ELECTRON DENSITY MAPS NUMERING OF RESIDUES IS SUCH THAT IT IS CONSISTENT WITH THE RESIDUE NUMERING IN PDB ENTRY PDB1HXN.ENT 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: 1.92 Å3/Da / Density % sol: 35 %
Crystal growpH: 7.5
Details: HANGING DROP, 4 DEGREES CENTIGRADES, RESEVOIR SOLUTION: 19-22% PEG 4000, 0.05 M TRIS HCL PH 7.5, 0.05-0.5 M EDTA, 0.2 NACL PROTEIN COMPLEX SOLUTION: 40 MG/ ML IN 0.05 M TRIS PH 7.0 AND 0.2 M NACL
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
119-22 %(w/v)PEG40001reservoir
20.05 MTris-HCl1reservoir
30.05-0.5 MEDTA1reservoir
40.2 M1reservoirNaCl
540 mg/mlprotain1drop
60.05 MTris-HCl1drop
70.2 M1dropNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: CYCLINDRICALLY BENT TRIANGULAR SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 19233 / % possible obs: 94.7 % / Redundancy: 2.4 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.1 / % possible all: 77
Reflection
*PLUS
Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 77 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
CCP4AGROVATA-ROTAVATAdata reduction
AMoREphasing
MAMAmodel building
MAVEmodel building
REFMACrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
MAMAphasing
MAVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HXN AND 1FBL

1hxn

1fbl


Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 2.5 / ESU R: 1.29 / ESU R Free: 0.33
Details: ELECTRON DENSITY FOR RESIDUES ARG 214, SER 215 AND HIS 222 IS POORLY DEFINED
RfactorNum. reflection% reflectionSelection details
Rfree0.289 951 5 %RANDOM
Rwork0.207 ---
obs0.201 19233 94.7 %-
Displacement parametersBiso mean: 35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3199 0 54 210 3463
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0941.5
X-RAY DIFFRACTIONp_mcangle_it1.8392
X-RAY DIFFRACTIONp_scbond_it1.6972
X-RAY DIFFRACTIONp_scangle_it2.5062.5
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1830.3
X-RAY DIFFRACTIONp_multtor_nbd0.2110.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor17.720
X-RAY DIFFRACTIONp_staggered_tor23.830
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor2750
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 2.5 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35 Å2

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