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- PDB-1d9v: HAEMOPHILUS INFLUENZAE FERRIC-BINDING PROTEIN APO FORM -

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Basic information

Entry
Database: PDB / ID: 1d9v
TitleHAEMOPHILUS INFLUENZAE FERRIC-BINDING PROTEIN APO FORM
ComponentsPROTEIN (iron-utilization periplasmic protein)
KeywordsMETAL BINDING PROTEIN / FERRIC / BINDING PROTEIN / IRON / APO FORM / PERIPLASMIC PROTEIN / ABC CASSETTE RECEPTOR PROTEIN
Function / homology
Function and homology information


iron ion transport / transmembrane transport / periplasmic space / metal ion binding
Similarity search - Function
Ferric binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Iron-utilization periplasmic protein
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsMcRee, D.E. / Bruns, C.M. / Williams, P.A.
CitationJournal: Biochemistry / Year: 2001
Title: Crystallographic and biochemical analyses of the metal-free Haemophilus influenzae Fe3+-binding protein.
Authors: Bruns, C.M. / Anderson, D.S. / Vaughan, K.G. / Williams, P.A. / Nowalk, A.J. / McRee, D.E. / Mietzner, T.A.
History
DepositionOct 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (iron-utilization periplasmic protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8642
Polymers33,7691
Non-polymers951
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.746, 77.418, 34.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEIN (iron-utilization periplasmic protein)


Mass: 33769.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Description: GRAM-NEGATIVE HUMAN PATHOGENIC BACTERIA / Gene: HITA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P35755
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 1450, HEPES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 17K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
128 %PEG14501reservoir
2100 mMHEPES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→100 Å / Num. all: 27731 / Num. obs: 27731 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.059
Reflection shellResolution: 1.75→1.86 Å / Rmerge(I) obs: 0.37 / Num. unique all: 3703 / % possible all: 77
Reflection
*PLUS
Lowest resolution: 8 Å / Num. obs: 27754 / Redundancy: 6.7 %
Reflection shell
*PLUS
% possible obs: 77 % / Redundancy: 3.5 % / Num. unique obs: 3703

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Processing

Software
NameVersionClassification
TNTrefinement
XTALVIEWrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.75→100 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection
Rfree0.263 1400
Rwork0.179 -
all-27731
obs-27731
Refinement stepCycle: LAST / Resolution: 1.75→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 5 153 2550
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.2
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.22
LS refinement shell
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 1.86 Å / Rfactor Rfree: 0.38 / Rfactor obs: 0.37

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