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- PDB-1nnf: Crystal Structure Analysis of Haemophlius Influenzae Ferric-ion B... -

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Basic information

Entry
Database: PDB / ID: 1nnf
TitleCrystal Structure Analysis of Haemophlius Influenzae Ferric-ion Binding Protein H9Q Mutant Form
ComponentsIron-utilization periplasmic protein
KeywordsMETAL BINDING PROTEIN / IRON-BINDING PROTEIN / EDTA-FE-PROTEIN COMPLEX
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
Chem-EDT / : / Iron-utilization periplasmic protein
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsShouldice, S.R. / Dougan, D.R. / Skene, R.J. / Tari, L.W. / McRee, D.E. / Yu, R.-H. / Schryvers, A.B.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: High Resolution Structure of an Alternate Form of the Ferric ion Binding Protein from Haemophilus influenzae
Authors: Shouldice, S.R. / Dougan, D.R. / Skene, R.J. / Tari, L.W. / McRee, D.E. / Yu, R.-H. / Schryvers, A.B.
History
DepositionJan 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron-utilization periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1073
Polymers33,7591
Non-polymers3482
Water6,467359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.101, 75.344, 33.503
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 Iron-utilization periplasmic protein / Major ferric iron binding protein / FBP / Iron-regulated 40 kDa protein / MIRP / Fe(+3)-binding protein


Mass: 33759.230 Da / Num. of mol.: 1 / Mutation: H9Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HITA / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P35755
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID


Mass: 292.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 1.74 Å3/Da / Density % sol: 28.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: PEG 5000, Tris HCl, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %(w/v)PEG50001drop
250 mMTris-HCl1droppH8.2
320 %PEG50001reservoir
4100 mMTris-HCl1reservoirpH8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 29, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→105.41 Å / Num. obs: 89423
Reflection shellResolution: 1.1→1.14 Å / Rsym value: 0.199 / % possible all: 36.1
Reflection
*PLUS
% possible obs: 86.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 36.1 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 5.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
MOLREPphasing
REFMAC5.1.19refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D9V

1d9v


Resolution: 1.1→105.41 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.428 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.038 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1804 4721 5 %RANDOM
Rwork0.15823 ---
all0.1594 89423 --
obs0.15934 89423 86.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.042 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.1→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 21 359 2722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212403
X-RAY DIFFRACTIONr_bond_other_d0.0020.022168
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.9673258
X-RAY DIFFRACTIONr_angle_other_deg0.90135075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45307
X-RAY DIFFRACTIONr_chiral_restr0.070.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022696
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02442
X-RAY DIFFRACTIONr_nbd_refined0.2070.2577
X-RAY DIFFRACTIONr_nbd_other0.2420.22797
X-RAY DIFFRACTIONr_nbtor_other0.0870.21441
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0810.241
X-RAY DIFFRACTIONr_mcbond_it0.9381.51529
X-RAY DIFFRACTIONr_mcangle_it1.50622434
X-RAY DIFFRACTIONr_scbond_it2.1653874
X-RAY DIFFRACTIONr_scangle_it3.3464.5824
LS refinement shellResolution: 1.1→1.127 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.214 130
Rwork0.173 2541
Refinement
*PLUS
Rfactor Rwork: 0.1582
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.257

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