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- PDB-5ec6: The apo crystal structure of haemoglobin receptor HpuA from Kinge... -

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Basic information

Entry
Database: PDB / ID: 5ec6
TitleThe apo crystal structure of haemoglobin receptor HpuA from Kingella denitrificans
ComponentsHemoglobin-haptoglobin-utilization protein
KeywordsMETAL TRANSPORT / Outer membrane / lipoprotein / receptor / beta barrel
Function / homologyHaemoglobin-haptoglobin utilisation, porphyrin transporter / Haemoglobin-haptoglobin utilisation, porphyrin transporter / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / cell outer membrane / Transferrin-binding protein B C-lobe/N-lobe beta barrel domain-containing protein
Function and homology information
Biological speciesKingella denitrificans ATCC 33394 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsWong, C.T. / Garnett, J.A. / 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 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 2.0Sep 13, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Aug 21, 2019Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 2.2Oct 23, 2019Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 3.0Mar 15, 2023Group: Advisory / Database references ...Advisory / Database references / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin-haptoglobin-utilization protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9823
Polymers33,7981
Non-polymers1842
Water5,855325
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint2 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.470, 102.470, 77.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Hemoglobin-haptoglobin-utilization protein


Mass: 33798.250 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 100 mM imidazole, 150 mM lithium sulfate, 6% Peg 3000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0411.008
SYNCHROTRONDiamond I0421.605
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELAug 2, 2014
DECTRIS PILATUS 6M2PIXELAug 2, 2014Cobalt SAD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0081
21.6051
ReflectionRedundancy: 18.8 % / Number: 588372 / Rsym value: 0.14 / D res high: 1.944 Å / D res low: 73.115 Å / Num. obs: 31296 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
6.1528.6810.0670.06718.8
4.356.1510.0770.07718.8
3.554.3510.0960.09620.2
3.073.5510.1020.10219.4
2.753.0710.1330.13319
2.512.7510.1810.18118.6
2.322.5110.2680.26818.6
2.172.3210.3420.34218.9
2.052.1710.4370.43718.7
1.942.0510.6710.67117.9
ReflectionResolution: 1.6→72.457 Å / Num. all: 54716 / Num. obs: 54716 / % possible obs: 100 % / Redundancy: 11.4 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.107 / Rsym value: 0.102 / Net I/av σ(I): 4.179 / Net I/σ(I): 12.6 / Num. measured all: 622672
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.6-1.6911.40.8532.88980578720.2620.8532.8100
1.69-1.7911.20.5291.48321474470.1650.5294.1100
1.79-1.9111.30.3112.47918970160.0960.3116.6100
1.91-2.0711.30.1893.87449465700.0580.18910.2100
2.07-2.2611.30.13956848860470.0430.13913.7100
2.26-2.5311.70.1175.86456454980.0360.11716.4100
2.53-2.9211.60.0926.95669948880.0280.09220.2100
2.92-3.5811.70.0856.94864341720.0260.08525.6100
3.58-5.0611.30.0777.93700032850.0240.07728.4100
5.06-26.41810.70.0588.52057619210.0190.05825.999.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.21data scaling
autoSHARPphasing
REFMAC5.8.0069refinement
PDB_EXTRACT3.15data extraction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→72.457 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.43 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.196 2686 4.9 %RANDOM
Rwork0.1706 ---
obs0.1719 51939 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.03 Å2 / Biso mean: 25.184 Å2 / Biso min: 13.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2--0.81 Å20 Å2
3----1.63 Å2
Refinement stepCycle: final / Resolution: 1.6→72.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 12 325 2566
Biso mean--48.52 34.14 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192342
X-RAY DIFFRACTIONr_bond_other_d0.0010.022156
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9613191
X-RAY DIFFRACTIONr_angle_other_deg0.81134992
X-RAY DIFFRACTIONr_chiral_restr0.0970.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212731
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02527
X-RAY DIFFRACTIONr_mcbond_it1.9472.2981227
X-RAY DIFFRACTIONr_mcbond_other1.9392.2951226
X-RAY DIFFRACTIONr_mcangle_it3.0143.4321536
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 212 -
Rwork0.266 3771 -
all-3983 -
obs--99.85 %

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