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- PDB-4rt6: Structure of a complex between hemopexin and hemopexin binding protein -

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Basic information

Entry
Database: PDB / ID: 4rt6
TitleStructure of a complex between hemopexin and hemopexin binding protein
Components
  • Heme/hemopexin-binding protein
  • Hemopexin
KeywordsPROTEIN BINDING / beta-helix / beta-propeller domain / interaction of HxuA with hemopexin enables heme release from hemopexin / outer membrane
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 / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain ...Hemopexin / 4 Propeller / Hemopexin / Hemopexin-like domain / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Pectin lyase fold / Pectin lyase fold/virulence factor / Mainly Beta
Similarity search - Domain/homology
Hemopexin / Heme/hemopexin-binding protein
Similarity search - Component
Biological speciesHaemophilus influenzae Rd KW20 (bacteria)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZambolin, S. / Clantin, B. / Haouz, A. / Villeret, V. / Delepelaire, P.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis for haem piracy from host haemopexin by Haemophilus influenzae.
Authors: Zambolin, S. / Clantin, B. / Chami, M. / Hoos, S. / Haouz, A. / Villeret, V. / Delepelaire, P.
History
DepositionNov 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heme/hemopexin-binding protein
B: Hemopexin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4883
Polymers121,0642
Non-polymers4241
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-4 kcal/mol
Surface area38120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.060, 348.860, 77.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailscomplex between HxuA and hemopexin N-terminal domain

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Components

#1: Protein Heme/hemopexin-binding protein / Heme:hemopexin utilization protein A


Mass: 96594.391 Da / Num. of mol.: 1 / Mutation: C876S, C882S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria)
Strain: Rd KW20 / Gene: hxuA, HI_0264 / Plasmid: pBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P44602
#2: Protein Hemopexin /


Mass: 24469.361 Da / Num. of mol.: 1 / Fragment: N-Terminal domain / Source method: isolated from a natural source / Details: purified from rabbit blood serum / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P20058
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100mM citric acid, 25% w/v PEG 4000, 200mM ammonium sulfate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2014
RadiationMonochromator: CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. all: 31168 / Num. obs: 30025 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 74.96 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.8-2.97185.2
2.97-3.18193.8
3.18-3.43198.5
3.43-3.76199.5

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Processing

Software
NameVersionClassification
XDSdata reduction
AMoREphasing
BUSTER2.10.1refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 4RM6, 1QHU

4rm6

1qhu


Resolution: 2.8→24.43 Å / Cor.coef. Fo:Fc: 0.9199 / Cor.coef. Fo:Fc free: 0.8812 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 1517 5.06 %RANDOM
Rwork0.1796 ---
all0.1821 31236 --
obs0.1821 29966 96.03 %-
Displacement parametersBiso mean: 55.54 Å2
Baniso -1Baniso -2Baniso -3
1-16.0538 Å20 Å20 Å2
2---7.4691 Å20 Å2
3----8.5848 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.8→24.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7621 0 28 192 7841
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017774HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2210484HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3683SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes245HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1107HARMONIC5
X-RAY DIFFRACTIONt_it7774HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.88
X-RAY DIFFRACTIONt_other_torsion3.17
X-RAY DIFFRACTIONt_chiral_improper_torsion1042SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8494SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.9 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3517 114 4.83 %
Rwork0.2562 2247 -
all0.261 2361 -
obs--96.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4173-0.16060.24390.4969-0.24381.282-0.0158-0.0403-0.12590.04640.077-0.0407-0.1079-0.1368-0.06120.0872-0.0320.003-0.23490.0205-0.1958-11.295460.0741-25.0961
22.3068-0.7004-1.05853.63850.92220.76140.0001-0.0741-0.85040.08330.0527-0.47340.20150.0766-0.05280.075-0.0122-0.0818-0.3884-0.03170.459512.504318.5777-10.6096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 815
2X-RAY DIFFRACTION2{ B|* }B24 - 208

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