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

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Basic information

Entry
Database: PDB / ID: 3csl
TitleStructure of the Serratia marcescens hemophore receptor HasR 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 / 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
PROTOPORPHYRIN IX CONTAINING FE / Hemophore HasA / HasR protein
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 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

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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)234,83413
Polymers232,9564
Non-polymers1,8789
Water77543
1
A: HasR protein
C: Hemophore HasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,5558
Polymers116,4782
Non-polymers1,0776
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-45.8 kcal/mol
Surface area35050 Å2
MethodPISA
2
B: HasR protein
D: Hemophore HasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2795
Polymers116,4782
Non-polymers8013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-41.3 kcal/mol
Surface area34870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.020, 163.400, 595.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 4.1 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2 M NaCl, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2911
SYNCHROTRONSLS X06SA20.97152,0.97897,0.97921
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 29, 2006
MARMOSAIC 225 mm CCD2CCDNov 24, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)monochromatorSINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.971521
30.978971
40.979211
ReflectionResolution: 2.56→49.174 Å / Num. obs: 111662 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.03 % / Biso Wilson estimate: 48.146 Å2 / Rmerge(I) obs: 0.164 / Net I/σ(I): 10.21
Reflection shellResolution: 2.56→2.71 Å / Redundancy: 2.81 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 1.59 / % possible all: 63.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→49.174 Å / SU ML: 0.43 / Isotropic thermal model: isotropic and tls / Phase error: 29.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2739 4959 4.99 %
Rwork0.2389 --
obs0.2406 99334 95.03 %
all-99334 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.003 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso mean: 93.25 Å2
Baniso -1Baniso -2Baniso -3
1--19.117 Å2-0 Å20 Å2
2---12.415 Å20 Å2
3---8.215 Å2
Refine analyzeLuzzati coordinate error obs: 1.32 Å
Refinement stepCycle: LAST / Resolution: 2.7→49.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14146 0 128 43 14317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114637
X-RAY DIFFRACTIONf_angle_d0.53519881
X-RAY DIFFRACTIONf_dihedral_angle_d11.6365094
X-RAY DIFFRACTIONf_chiral_restr0.0372082
X-RAY DIFFRACTIONf_plane_restr0.0022632
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.7310.3841040.3492329243371
2.731-2.7630.3661420.3422463260575
2.763-2.7960.4131320.3492486261877
2.796-2.8320.371290.3562697282680
2.832-2.8690.3941440.3452666281083
2.869-2.9080.3521330.352922305587
2.908-2.950.4031650.3532979314492
2.95-2.9940.3731600.343118327894
2.994-3.0410.3531740.3463172334697
3.041-3.0910.4111620.3213222338498
3.091-3.1440.361790.2983285346499
3.144-3.2010.3431720.2993221339399
3.201-3.2630.3081950.28532683463100
3.263-3.3290.3251700.28433353505100
3.329-3.4020.3281890.27832343423100
3.402-3.4810.2891760.26232833459100
3.481-3.5680.2951720.24233143486100
3.568-3.6640.2911700.23233013471100
3.664-3.7720.2671710.22733143485100
3.772-3.8940.2551640.21933123476100
3.894-4.0330.2731780.22232873465100
4.033-4.1940.2621580.233403498100
4.194-4.3850.2311900.18632853475100
4.385-4.6160.171650.16833203485100
4.616-4.9050.1931840.1633363520100
4.905-5.2830.1861930.16532983491100
5.283-5.8140.1851870.16733343521100
5.814-6.6540.1841640.17633873551100
6.654-8.3760.2251740.18233773551100
8.376-49.1820.2611630.2353490365399
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)
10.676-0.6641-0.5917-0.1763-0.92110.6881-0.05360.0828-0.12950.17580.1913-0.07070.2998-0.39870.220.7437-0.5526-0.03410.3418-0.05670.100149.310256.1503236.8621
20.5592-0.26710.5440.84120.30840.88460.2540.0596-0.02750.1566-0.02810.1245-0.18530.137-0.10870.3884-0.39730.07940.7323-0.02130.142794.45059.0859210.5676
33.4162.4603-0.4164-0.18871.30737.2892-0.3110.75660.01510.170.133-0.1956-1.0511-1.18220.11761.5369-0.0507-0.03261.56290.31781.063936.309948.0198269.2206
40.89210.6297-0.94212.27534.2379-5.90490.2538-0.8213-0.1166-0.1086-0.45870.2261-0.49980.58920.14471.5715-0.7492-0.28391.74910.17531.031484.6145-3.5441178.5373
50.675-0.1672-0.05830.8713-0.03591.7848-0.0309-0.1865-0.04940.48390.1461-0.1261-0.0511-0.14890.10540.4782-0.3442-0.06180.4179-0.02470.138156.995367.6501245.6928
60.5825-0.14190.10940.54680.05332.15370.24860.35610.1819-0.0397-0.0446-0.03-0.24670.4179-0.03680.3861-0.36590.06570.61760.01380.1361106.07116.106201.3483
7-0.0792-0.3272-0.49770.7767-0.14971.5635-0.08480.1337-0.01540.4139-0.00260.1270.3474-0.09040.07591.3129-0.26-0.03120.7474-0.0030.288254.55860.2206286.8761
81.1886-0.41360.64590.5782-0.26170.22310.12450.3983-0.0656-0.0304-0.0833-0.019-0.4014-0.2563-0.06730.5645-0.11890.02081.25460.0190.227697.068813.7171160.4617
90.76550.09181.95010.93940.48463.0861-0.22340.1983-0.0461-0.19630.21080.07630.34410.1623-0.1290.5606-0.7091-0.4944-0.1006-0.48580.20847.96156.8546262.334
104.16053.37442.311.1442-0.76923.38380.7378-0.1835-0.78860.2802-0.5126-0.2339-0.21470.0394-0.23370.13780.2125-0.32360.360.6228-0.046194.44247.4783185.1516
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A113 - 417
2X-RAY DIFFRACTION2B113 - 417
3X-RAY DIFFRACTION3A418 - 423
4X-RAY DIFFRACTION4B418 - 423
5X-RAY DIFFRACTION5A424 - 865
6X-RAY DIFFRACTION6B424 - 865
7X-RAY DIFFRACTION7C113 - 0
8X-RAY DIFFRACTION8D113 - 0
9X-RAY DIFFRACTION9A872 - 906
10X-RAY DIFFRACTION10B869 - 888

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