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- PDB-4i84: The crystal structure of the Haemophilus influenzae HxuA secretio... -

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Basic information

Entry
Database: PDB / ID: 4i84
TitleThe crystal structure of the Haemophilus influenzae HxuA secretion domain involved in the two-partner secretion pathway
ComponentsHeme/hemopexin-binding protein
KeywordsPROTEIN TRANSPORT / beta-helix / TWO-PARTNER SECRETION PATHWAY / HxuB
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Heme/hemopexin-binding protein
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBaelen, S. / Dewitte, F. / Clantin, B. / Villeret, V.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of the secretion domain of HxuA from Haemophilus influenzae.
Authors: Baelen, S. / Dewitte, F. / Clantin, B. / Villeret, V.
History
DepositionDec 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heme/hemopexin-binding protein
B: Heme/hemopexin-binding protein


Theoretical massNumber of molelcules
Total (without water)65,9352
Polymers65,9352
Non-polymers00
Water7,728429
1
A: Heme/hemopexin-binding protein


Theoretical massNumber of molelcules
Total (without water)32,9681
Polymers32,9681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heme/hemopexin-binding protein


Theoretical massNumber of molelcules
Total (without water)32,9681
Polymers32,9681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.990, 70.840, 104.980
Angle α, β, γ (deg.)90.00, 98.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heme/hemopexin-binding protein / Heme:hemopexin utilization protein A


Mass: 32967.695 Da / Num. of mol.: 2 / Fragment: UNP residues 24-324
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: HI_0264, hxuA, KW20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)omp5 / References: UniProt: P44602
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.095M TRI SODIUM CITRATE pH 5.6, 5% GLYCEROL, 19% ISOPROPANOL, 12% PEG4000, 0.5M IMIDAZOLE pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2011
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.5→41.9 Å / Num. all: 89861 / Num. obs: 89775 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.5→1.59 Å

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ODL

2odl


Resolution: 1.5→41.9 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.648 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.083 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21027 4489 5 %RANDOM
Rwork0.159 ---
obs0.16154 85287 100 %-
all-89815 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.866 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.08 Å2
2--0.01 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4278 0 0 429 4707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0224513
X-RAY DIFFRACTIONr_angle_refined_deg2.2361.9486127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1975617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.00327.5196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64315837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.897159
X-RAY DIFFRACTIONr_chiral_restr0.1560.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023369
X-RAY DIFFRACTIONr_mcbond_it2.8641.52933
X-RAY DIFFRACTIONr_mcangle_it4.24624772
X-RAY DIFFRACTIONr_scbond_it6.0931580
X-RAY DIFFRACTIONr_scangle_it9.2174.51342
X-RAY DIFFRACTIONr_rigid_bond_restr3.18634513
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 318 -
Rwork0.232 6044 -
obs--100 %

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