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- PDB-1mrp: FERRIC-BINDING PROTEIN FROM HAEMOPHILUS INFLUENZAE -

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Basic information

Entry
Database: PDB / ID: 1mrp
TitleFERRIC-BINDING PROTEIN FROM HAEMOPHILUS INFLUENZAE
ComponentsFERRIC IRON BINDING PROTEIN
KeywordsIRON TRANSPORT / FERRIC IRON BINDING PROTEIN / PERIPLASMIC BINDING PROTEIN / TRANSFERRIN SUPERFAMILY
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 / MIR / Resolution: 1.6 Å
AuthorsBruns, C.M. / Nowalk, A.J. / Arvai, A.S. / Mctigue, M.A. / Vaughan, K.G. / Mietzner, T.A. / Mcree, D.E.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of Haemophilus influenzae Fe(+3)-binding protein reveals convergent evolution within a superfamily.
Authors: Bruns, C.M. / Nowalk, A.J. / Arvai, A.S. / McTigue, M.A. / Vaughan, K.G. / Mietzner, T.A. / McRee, D.E.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: Biochemical Characterization of a Haemophilus Influenzae Periplasmic Iron Transport Operon
Authors: Adhikari, P. / Kirby, S.D. / Nowalk, A.J. / Veraldi, K.L. / Schryvers, A.B. / Mietzner, T.A.
#2: Journal: Biochemistry / Year: 1994
Title: Coordination of Iron by the Ferric Iron-Binding Protein of Pathogenic Neisseria is Homologous to the Transferrins
Authors: Nowalk, A.J. / Tencza, S.B. / Mietzner, T.A.
History
DepositionMay 14, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _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: FERRIC IRON BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9203
Polymers33,7691
Non-polymers1512
Water2,990166
1
A: FERRIC IRON BINDING PROTEIN
hetero molecules

A: FERRIC IRON BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8406
Polymers67,5392
Non-polymers3024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)132.194, 52.449, 41.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-469-

HOH

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Components

#1: Protein FERRIC IRON BINDING PROTEIN / FBP / HITA / HFBP / MAJOR IRON REGULATED PROTEIN / MIRP


Mass: 33769.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Cellular location: PERIPLASMIC SPACE / Gene: HITA / Plasmid: PBSJ1 / Gene (production host): HITA / Production host: Escherichia coli (E. coli) / Strain (production host): H-1443 / 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-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.12 Å3/Da / Density % sol: 35 %
Crystal growpH: 6.6
Details: 20% PEG 4000, 400 MM IMIDAZOLE/MALATE PH 6.6, 200 MM NACL
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG40001reservoir
2200 mM1reservoirNaCl
3400 mMimidazole/malate1reservoir

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1996 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 36442 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.072 / Net I/σ(I): 27.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.54 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.282 / % possible all: 54
Reflection
*PLUS
Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 54 % / Rmerge(I) obs: 0.282

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Processing

Software
NameVersionClassification
PHASESphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.6→50 Å / Isotropic thermal model: TNT BCORREL V1.0
Cross valid method: THROUGHOUT, EXCEPT FINAL ROUND OF REFINEMENT
σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rfree0.24 3163 8.7 %
Rwork0.174 --
all0.179 36442 -
obs0.179 36442 93.3 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 182.5 Å2 / ksol: 0.79 e/Å3
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 6 166 2618
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01525260.8
X-RAY DIFFRACTIONt_angle_deg2.1234041.5
X-RAY DIFFRACTIONt_dihedral_angle_d16.3915290
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.015701
X-RAY DIFFRACTIONt_gen_planes0.023603
X-RAY DIFFRACTIONt_it4.2425221.3
X-RAY DIFFRACTIONt_nbd0.0275410
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_angle_deg2.28
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.390
X-RAY DIFFRACTIONt_plane_restr0.023
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.66 Å / Rfactor all: 0.36

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