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- PDB-5c58: A double mutant of serratia marcescens hemophore receptor HasR in... -

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Basic information

Entry
Database: PDB / ID: 5c58
TitleA double mutant of serratia marcescens hemophore receptor HasR in complex with its hemophore HasA and heme
Components
  • HasR protein
  • Hemophore HasA
KeywordsTRANSPORT PROTEIN / outer membrane receptor / transporter complex / heme transfer
Function / homology
Function and homology information


heme transmembrane transporter activity / cell outer membrane / extracellular region / metal ion binding
Similarity search - Function
TonB-dependent haem/haemoglobin receptor / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / Heme-binding Protein A; Chain: A; / Haem-binding HasA / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / Haem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) ...TonB-dependent haem/haemoglobin receptor / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / Heme-binding Protein A; Chain: A; / Haem-binding HasA / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / Haem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / Beta Complex / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemophore HasA / HasR protein
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.795 Å
AuthorsBecker, S. / Diederichs, K. / Welte, W.
CitationJournal: Eur.Biophys.J. / Year: 2020
Title: Binding of HasA by its transmembrane receptor HasR follows a conformational funnel mechanism.
Authors: Exner, T.E. / Becker, S. / Becker, S. / Boniface-Guiraud, A. / Delepelaire, P. / Diederichs, K. / Welte, W.
History
DepositionJun 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: HasR protein
B: Hemophore HasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,9653
Polymers116,3492
Non-polymers6161
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-30 kcal/mol
Surface area35340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.971, 114.619, 260.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein HasR protein


Mass: 94825.602 Da / Num. of mol.: 1 / Mutation: R297A, N800A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: hasR / Production host: Escherichia coli (E. coli) / References: UniProt: Q79AD2
#2: Protein Hemophore HasA / Heme acquisition system protein A


Mass: 21523.205 Da / Num. of mol.: 1 / Fragment: UNP residues 2-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: hasA / Production host: Escherichia coli (E. coli) / References: UniProt: Q54450
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100mM Tris pH 7 to 8, 1.8 to 2.2mM NaCl, 100mM K2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→40 Å / Num. obs: 37882 / % possible obs: 99 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.095 / Rsym value: 0.103 / Net I/σ(I): 13.26
Reflection shellResolution: 2.79→2.96 Å / Redundancy: 5.9 % / Rmerge(I) obs: 2.227 / Mean I/σ(I) obs: 0.91 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX(1.10pre-2083_1692: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CSL, 1DK0

3csl

1dk0


Resolution: 2.795→37.749 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 37.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2964 1882 4.98 %
Rwork0.2471 --
obs0.2496 37807 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.795→37.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6482 0 43 0 6525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036679
X-RAY DIFFRACTIONf_angle_d0.6679079
X-RAY DIFFRACTIONf_dihedral_angle_d15.2293873
X-RAY DIFFRACTIONf_chiral_restr0.031962
X-RAY DIFFRACTIONf_plane_restr0.0031196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7947-2.87030.47371220.45342458X-RAY DIFFRACTION89
2.8703-2.95470.42511390.38492753X-RAY DIFFRACTION100
2.9547-3.050.35781340.35212747X-RAY DIFFRACTION100
3.05-3.1590.39121530.32472766X-RAY DIFFRACTION100
3.159-3.28540.35021440.30452751X-RAY DIFFRACTION100
3.2854-3.43480.31331350.26352778X-RAY DIFFRACTION100
3.4348-3.61580.31431390.24132758X-RAY DIFFRACTION99
3.6158-3.84210.31481260.24942801X-RAY DIFFRACTION100
3.8421-4.13840.33321610.24132741X-RAY DIFFRACTION100
4.1384-4.55420.25231490.21012802X-RAY DIFFRACTION100
4.5542-5.21180.25631550.19742810X-RAY DIFFRACTION100
5.2118-6.56070.28081620.23732818X-RAY DIFFRACTION100
6.5607-37.75280.26771630.23162942X-RAY DIFFRACTION99
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)
11.81280.48720.84341.0219-0.31911.3085-0.05150.05430.0087-0.1095-0.0237-0.02370.11120.16070.08210.45870.0301-0.00761.0339-0.19630.7001-15.465224.364753.0491
21.1704-0.14980.32940.9824-0.95421.8323-0.13240.18960.1381-0.26220.09830.14260.1137-0.59560.07980.55260.0233-0.09821.0419-0.06510.6849-35.592827.373641.4136
31.9809-0.0111-0.42281.82620.44211.76470.2397-0.01870.08650.1003-0.1660.15540.34820.3047-0.19940.6340.117-0.04060.75350.02340.9515-16.26072.946258.6227
41.45890.36660.37041.66860.51891.4652-0.03330.7121-0.1449-0.58330.391-0.03350.9058-0.1095-0.33041.1541-0.13010.05481.8564-0.11870.6593-31.868717.80233.6661
56.1746-0.045-0.79085.3793.67762.61980.01750.6362-0.0516-0.11870.8187-0.20830.5467-1.5269-0.63881.15110.0730.00861.8744-0.09360.5729-40.215722.31345.2736
60.32470.11620.4460.87810.39841.5172-0.15390.23770.1948-0.30830.4504-0.55240.19930.3727-0.32421.3607-0.0408-0.07311.9948-0.11310.6795-34.442812.2105-4.9079
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 113:485)
2X-RAY DIFFRACTION2(chain A and resid 486:752)
3X-RAY DIFFRACTION3(chain A and resid 759:865)
4X-RAY DIFFRACTION4(chain B and resid 2:90)
5X-RAY DIFFRACTION5(chain B and resid 91:103)
6X-RAY DIFFRACTION6(chain B and resid 104:174)

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