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- PDB-3ddr: Structure of the Serratia marcescens hemophore receptor HasR-Ile6... -

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Basic information

Entry
Database: PDB / ID: 3ddr
TitleStructure of the Serratia marcescens hemophore receptor HasR-Ile671Gly mutant in complex with its hemophore HasA and heme
Components
  • HasR protein
  • Hemophore HasA
KeywordsMEMBRANE PROTEIN/HEME BINDING PROTEIN / outer membrane protein / beta-barrel / hemophore receptor / Membrane / Outer membrane / TonB box / Heme / Iron / Metal-binding / Secreted / MEMBRANE PROTEIN-HEME BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


heme transmembrane transporter activity / siderophore uptake 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 / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / 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 / Difference fourier / Resolution: 2.8 Å
AuthorsKrieg, S. / Diederichs, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Heme uptake across the outer membrane as revealed by crystal structures of the receptor-hemophore complex.
Authors: Krieg, S. / Huche, F. / Diederichs, K. / Izadi-Pruneyre, N. / Lecroisey, A. / Wandersman, C. / Delepelaire, P. / Welte, W.
History
DepositionJun 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Mar 21, 2012Group: Database references
Revision 1.4Oct 25, 2017Group: Refinement description / Category: software
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HasR protein
B: HasR protein
C: Hemophore HasA
D: Hemophore HasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,67514
Polymers232,8444
Non-polymers1,83210
Water23413
1
A: HasR protein
C: Hemophore HasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,1535
Polymers116,4222
Non-polymers7323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-38 kcal/mol
Surface area35560 Å2
MethodPISA
2
B: HasR protein
D: Hemophore HasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,5229
Polymers116,4222
Non-polymers1,1007
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-39 kcal/mol
Surface area35610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.410, 162.720, 597.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11B-873-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 113:865 )
21chain B and (resseq 113:865 )
12chain C and (resseq 2:28 or resseq 42:173 )
22chain D and (resseq 2:28 or resseq 42:173 )

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111AA113 - 865113 - 865
211BB113 - 865113 - 865
112CC2 - 282 - 28
122CC42 - 17342 - 173
212DD2 - 282 - 28
222DD42 - 17342 - 173

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein HasR protein


Mass: 94898.641 Da / Num. of mol.: 2 / Fragment: UNP residues 48 to 899 / Mutation: I671G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: hasR / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): MC4100 / References: UniProt: Q79AD2
#2: Protein Hemophore HasA / Heme acquisition system protein A


Mass: 21523.205 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: hasA / Plasmid: pQE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q54450

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Non-polymers , 4 types, 23 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THERE IS AN ERROR IN THE DATABASE SEQUENCE

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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: 4.1 Å3/Da / Density % sol: 74.26 %
Crystal growTemperature: 291 K / pH: 8
Details: 2 M NaCl, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0162
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 5, 2008
RadiationMonochromator: Si(111)monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0162 Å / Relative weight: 1
ReflectionResolution: 2.8→39.4 Å / Num. all: 92482 / Num. obs: 92482 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.66 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 14.03
Reflection shellResolution: 2.8→2.96 Å / Redundancy: 5.55 % / Rmerge(I) obs: 0.1977 / Mean I/σ(I) obs: 0.89 / % possible all: 88.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: Difference fourier / Resolution: 2.8→39.25 Å / SU ML: 0.4 / Isotropic thermal model: isotropic and tls / σ(F): 1.99 / Phase error: 33.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 4636 5.01 %
Rwork0.226 --
obs0.227 92482 98.1 %
all-92482 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.22 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso mean: 104.79 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.653 Å
Refinement stepCycle: LAST / Resolution: 2.8→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14122 0 124 13 14259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614588
X-RAY DIFFRACTIONf_angle_d1.07819838
X-RAY DIFFRACTIONf_dihedral_angle_d17.4835080
X-RAY DIFFRACTIONf_chiral_restr0.0772076
X-RAY DIFFRACTIONf_plane_restr0.0042626
LS refinement shellResolution: 2.8→2.83 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.483 111 -
Rwork0.466 2123 -
obs--71 %
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)
10.2879-0.1806-0.25990.32020.02050.5367-0.16560.0224-0.03120.10830.0519-0.04140.0533-0.67780.07730.3634-0.49760.01291.2801-0.03810.060949.296855.9919237.5332
20.6537-0.1925-0.4750.20840.2537-0.26460.15280.02360.1130.1106-0.17480.0178-0.23810.66480.02140.3367-0.40010.07151.3436-0.08130.12794.51469.2239210.8499
30.3123-0.4039-0.14811.3853-0.862-0.0837-0.0463-0.3438-0.00970.5070.2280.3063-0.3806-0.4108-0.23360.4058-0.4466-0.12331.3811-0.0897-0.021549.410176.5193247.0173
40.06810.0250.67820.4703-0.47480.9630.14210.12530.01780.0339-0.07870.09620.02881.757-0.07510.5232-0.51920.07042.2652-0.09860.2199114.76688.2433200.8328
50.4657-0.25320.27191.246-0.40410.398-0.1845-0.27850.11720.58450.0413-0.1621-0.1892-0.00530.00280.0725-0.40640.00481.1138-0.01950.049262.183960.5655246.1301
60.9476-0.60850.62670.4620.05420.23410.24490.69240.1767-0.189-0.186-0.0984-0.57450.2759-0.02650.482-0.48760.10061.1542-0.00820.097799.512621.8194202.0639
70.2883-0.41462.16540.8225-0.0905-3.5078-0.04960.0331-0.01280.58560.00090.02730.2713-0.45470.03981.206-0.3520.01081.68540.06760.135754.631859.578287.1645
8-0.0062-0.0693-0.31210.1636-0.58410.63490.1311-0.0335-0.0757-0.0357-0.08250.0154-0.1908-0.2159-0.06190.8827-0.1081-0.03692.33420.05680.338496.965113.9544161.1411
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A113 - 418
2X-RAY DIFFRACTION2B113 - 418
3X-RAY DIFFRACTION3A419 - 607
4X-RAY DIFFRACTION4B419 - 607
5X-RAY DIFFRACTION5A608 - 865
6X-RAY DIFFRACTION6B608 - 865
7X-RAY DIFFRACTION7C1 - 200
8X-RAY DIFFRACTION8D1 - 200

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