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- PDB-3csn: Structure of the Serratia marcescens hemophore receptor HasR in c... -

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Basic information

Entry
Database: PDB / ID: 3csn
TitleStructure of the Serratia marcescens hemophore receptor HasR in complex with its hemophore HasA
Components
  • HasR protein
  • Hemophore HasA
KeywordsMEMBRANE PROTEIN/HEME BINDING PROTEIN / outer membrane protein / beta-barrel / hemophore receptor / TonB box / Heme / Iron / Metal-binding / Secreted / MEMBRANE PROTEIN-HEME BINDING PROTEIN COMPLEX
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
Hemophore HasA / HasR protein
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference fourier / Resolution: 3 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
DepositionApr 10, 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 1.2Mar 21, 2012Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software

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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)233,4169
Polymers232,9564
Non-polymers4605
Water34219
1
A: HasR protein
C: Hemophore HasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5703
Polymers116,4782
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-16.8 kcal/mol
Surface area35620 Å2
MethodPISA
2
B: HasR protein
D: Hemophore HasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8466
Polymers116,4782
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-19.4 kcal/mol
Surface area35620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.650, 164.740, 597.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 113:865 )A113 - 865
211chain B and (resseq 113:865 )B113 - 865
112chain C and (resseq 1:28 or resseq 39:173 )C1 - 28
122chain C and (resseq 1:28 or resseq 39:173 )C39 - 173
212chain D and (resseq 1:28 or resseq 39:173 )D1 - 28
222chain D and (resseq 1:28 or resseq 39:173 )D39 - 173

NCS ensembles :
ID
1
2

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Components

#1: Protein HasR protein


Mass: 94954.742 Da / Num. of mol.: 2
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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
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: 4.16 Å3/Da / Density % sol: 74.58 %
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: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2007
RadiationMonochromator: Si(111)monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→49.4 Å / Num. obs: 77295 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.46 % / Biso Wilson estimate: 62.29 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 9.79
Reflection shellResolution: 3→3.2 Å / Redundancy: 5.13 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 2.15 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: Difference fourier / Resolution: 3→49.43 Å / Isotropic thermal model: isotropic and tls / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 3890 5.03 %
Rwork0.217 --
obs0.219 77295 99.2 %
all-77295 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.08 Å2
Baniso -1Baniso -2Baniso -3
1--7.919 Å20 Å2-0 Å2
2--7.658 Å2-0 Å2
3----17.707 Å2
Refine analyzeLuzzati coordinate error obs: 0.526 Å
Refinement stepCycle: LAST / Resolution: 3→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14146 0 30 19 14195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114505
X-RAY DIFFRACTIONf_angle_d1.12819703
X-RAY DIFFRACTIONf_dihedral_angle_d11.4615034
X-RAY DIFFRACTIONf_chiral_restr0.0682082
X-RAY DIFFRACTIONf_plane_restr0.0052618
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A5889X-RAY DIFFRACTIONPOSITIONAL0.08
12B5889X-RAY DIFFRACTIONPOSITIONAL0.08
21C1183X-RAY DIFFRACTIONPOSITIONAL0.059
22D1183X-RAY DIFFRACTIONPOSITIONAL0.059
LS refinement shellResolution: 3→3.03 Å / Total num. of bins used: 28
RfactorNum. reflection% reflection
Rfree0.383 136 -
Rwork0.375 2413 -
obs--93 %
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)
10.0079-0.0752-0.25040.3469-0.10180.1996-0.0618-0.0541-0.05760.11930.099-0.04420.2007-0.33560.05290.2828-0.29630.01130.20620.0290.140549.389856.654237.7612
20.22140.0396-0.1590.1119-0.05350.17450.11450.06270.04760.09730.00260.1353-0.14670.04320.11510.0886-0.23780.01880.3398-0.03210.112394.8099.022211.0411
30.3588-0.03570.31831.0949-0.47050.1565-0.006-0.2844-0.04290.49820.250.0834-0.3117-0.3618-0.16390.0681-0.3168-0.06460.0951-0.00690.043749.415377.2866247.1819
40.45270.14240.30470.0682-0.19480.870.08410.33620.04840.04760.05050.05820.25730.51-0.14950.2503-0.21930.00240.6667-0.04970.1849115.11017.8196200.9761
50.5251-0.12790.08220.9914-0.19670.1356-0.0829-0.2537-0.06680.51790.1459-0.1560.16440.2098-0.00990.1133-0.1954-0.08110.0994-0.04150.072262.245661.2869246.4349
60.9737-0.16930.16360.449-0.19720.27920.21750.49990.2173-0.1871-0.1460.0288-0.43110.08210.02510.1207-0.23390.06310.19920.03080.033899.90321.5547202.1583
7-0.0098-0.0824-0.09250.33120.04430.24980.02450.0376-0.04630.4484-0.18440.03110.2464-0.0050.10190.9647-0.1393-0.01260.5630.06310.198454.730560.9232287.753
80.2156-0.0769-0.02480.1408-0.21040.1928-0.0350.2593-0.02270.12370.0256-0.01860.0268-0.0497-0.01120.3861-0.0639-0.00251.1035-0.00530.230297.567913.7204160.9605
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 DIFFRACTION7C3 - 19
8X-RAY DIFFRACTION8D3 - 19

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