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- PDB-5ee4: The crystal structure of HpuA from Kingella denitrificans in comp... -

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Basic information

Entry
Database: PDB / ID: 5ee4
TitleThe crystal structure of HpuA from Kingella denitrificans in complex with human haemoglobin
Components
  • (Hemoglobin subunit ...) x 2
  • HpuA
KeywordsMETAL TRANSPORT / Outer membrane / receptor / beta barrel
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / cell outer membrane / oxygen carrier activity / carbon dioxide transport / Late endosomal microautophagy / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / response to hydrogen peroxide / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / regulation of blood pressure / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
Similarity search - Function
Haemoglobin-haptoglobin utilisation, porphyrin transporter / Haemoglobin-haptoglobin utilisation, porphyrin transporter / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin domain profile. ...Haemoglobin-haptoglobin utilisation, porphyrin transporter / Haemoglobin-haptoglobin utilisation, porphyrin transporter / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Transferrin-binding protein B C-lobe/N-lobe beta barrel domain-containing protein / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesKingella denitrificans ATCC 33394 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsWong, C.T. / Hare, S.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1100332 United Kingdom
CitationJournal: Nat Commun / Year: 2015
Title: Structural analysis of haemoglobin binding by HpuA from the Neisseriaceae family.
Authors: Wong, C.T. / Xu, Y. / Gupta, A. / Garnett, J.A. / Matthews, S.J. / Hare, S.A.
History
DepositionOct 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HpuA
B: HpuA
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,45616
Polymers129,6786
Non-polymers2,77810
Water6,738374
1
A: HpuA
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3209
Polymers64,8393
Non-polymers1,4816
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-59 kcal/mol
Surface area24590 Å2
MethodPISA
2
B: HpuA
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1367
Polymers64,8393
Non-polymers1,2974
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-61 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.790, 87.210, 124.320
Angle α, β, γ (deg.)90.000, 98.130, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22E
13D
23F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROVALVALAA15 - 32015 - 320
21PROPROVALVALBB15 - 32015 - 320
12VALVALARGARGCC1 - 1411 - 141
22VALVALARGARGEE1 - 1411 - 141
13GLUGLUTYRTYRDD6 - 1456 - 145
23GLUGLUTYRTYRFF6 - 1456 - 145

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HpuA


Mass: 33798.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kingella denitrificans ATCC 33394 (bacteria)
Gene: HMPREF9098_0447 / Production host: Escherichia coli (E. coli) / References: UniProt: F0EX68

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Hemoglobin subunit ... , 2 types, 4 molecules CEDF

#2: Protein Hemoglobin subunit alpha / Alpha-globin / Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: Blood / References: UniProt: P69905
#3: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: Blood / References: UniProt: P68871

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Non-polymers , 4 types, 384 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 1.92 Å3/Da / Density % sol: 35.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 100 mM Hepes, 18 % Peg 4,000, 10 % Isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.3→123.071 Å / Num. all: 49897 / Num. obs: 49897 / % possible obs: 96.9 % / Redundancy: 6.5 % / Rpim(I) all: 0.075 / Rrim(I) all: 0.191 / Rsym value: 0.175 / Net I/av σ(I): 3.467 / Net I/σ(I): 8.6 / Num. measured all: 322547
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.426.30.8182.14619972810.3530.8182.197.8
2.42-2.576.60.6241.24573969070.2610.6242.997.4
2.57-2.756.40.5461.14112564400.2360.5463.696.5
2.75-2.976.10.3122.43594058520.1350.3125.194.7
2.97-3.256.80.2133.53897757000.0880.2137.799.4
3.25-3.646.60.1474.33386451000.0620.14711.597.9
3.64-4.25.90.1074.52519642650.0480.10715.693.4
4.2-5.146.70.06410.32567838140.0260.06420.298.4
5.14-7.276.60.065101920229290.0270.0651897.6
7.27-41.1016.60.04910.71062716090.020.04925.895

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.49 Å41.1 Å
Translation6.49 Å41.1 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.21data scaling
PHASER2.5.6phasing
REFMAC5.8.0069refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EC6, 1HHO

5ec6

1hho


Resolution: 2.3→123.07 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.911 / SU B: 9.388 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.458 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 2491 5 %RANDOM
Rwork0.202 ---
obs0.2041 47357 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.52 Å2 / Biso mean: 33.173 Å2 / Biso min: 14.13 Å2
Baniso -1Baniso -2Baniso -3
1-2.65 Å20 Å2-0.13 Å2
2--0.11 Å20 Å2
3----2.62 Å2
Refinement stepCycle: final / Resolution: 2.3→123.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8742 0 192 374 9308
Biso mean--30.05 33.21 -
Num. residues----1164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199158
X-RAY DIFFRACTIONr_bond_other_d0.0050.028548
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.97812490
X-RAY DIFFRACTIONr_angle_other_deg1.04319673
X-RAY DIFFRACTIONr_chiral_restr0.0930.21393
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110476
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022115
X-RAY DIFFRACTIONr_mcbond_it2.3163.1884648
X-RAY DIFFRACTIONr_mcbond_other2.3163.1884647
X-RAY DIFFRACTIONr_mcangle_it3.5844.7735796
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A156220.13
12B156220.13
21C75990.12
22E75990.12
31D74030.12
32F74030.12
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 168 -
Rwork0.286 3501 -
all-3669 -
obs--97.66 %

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