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- PDB-2r79: Crystal Structure of a Periplasmic Heme Binding Protein from Pseu... -

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Basic information

Entry
Database: PDB / ID: 2r79
TitleCrystal Structure of a Periplasmic Heme Binding Protein from Pseudomonas aeruginosa
ComponentsPeriplasmic binding protein
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / heme transport
Function / homology
Function and homology information


: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Periplasmic binding protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsHo, W.W. / Li, H. / Poulos, T.L.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Holo- and apo-bound structures of bacterial periplasmic heme-binding proteins.
Authors: Ho, W.W. / Li, H. / Eakanunkul, S. / Tong, Y. / Wilks, A. / Guo, M. / Poulos, T.L.
History
DepositionSep 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Assembly

Deposited unit
A: Periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5876
Polymers29,5951
Non-polymers9935
Water2,846158
1
A: Periplasmic binding protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)183,52536
Polymers177,5686
Non-polymers5,95730
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
crystal symmetry operation10_774-y+2,-x+2,-z-1/21
crystal symmetry operation11_754-x+y+2,y,-z-1/21
crystal symmetry operation12_554x,x-y,-z-1/21
Buried area24130 Å2
ΔGint-253 kcal/mol
Surface area61010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.913, 132.913, 72.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Periplasmic binding protein


Mass: 29594.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 from ATCC / Plasmid: pET 101/D-TOPO / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O68879
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


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


Mass: 18.015 Da / Num. of mol.: 158 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate, 0.25M sodium chloride, 1.8M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL1-511
SYNCHROTRONSSRL BL1-521.74, 1.65
SYNCHROTRONSSRL BL1-531.74, 1.65
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDMar 23, 2007mirrors
ADSC QUANTUM 42CCDMar 23, 2007mirrors
ADSC QUANTUM 43CCDMar 24, 2007mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITEMADMx-ray2
3GRAPHITEMADMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.741
31.651
ReflectionResolution: 2.4→50 Å / Num. obs: 15023 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 24.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 735 / Rsym value: 0.53 / % possible all: 96.5

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→43.51 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3016812.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1476 9.8 %RANDOM
Rwork0.193 ---
obs0.193 15013 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.2989 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.35 Å20 Å20 Å2
2--4.35 Å20 Å2
3----8.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.4→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 65 158 2279
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scbond_it2.382
X-RAY DIFFRACTIONc_scangle_it3.62.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 221 9.1 %
Rwork0.223 2219 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2param19x.heme2water.top
X-RAY DIFFRACTION3water_rep.paramtoph19x.heme2
X-RAY DIFFRACTION4hetero.parhetero.top

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