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- PDB-1d9y: NEISSERIA GONORRHOEAE FERRIC BINDING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1d9y
TitleNEISSERIA GONORRHOEAE FERRIC BINDING PROTEIN
ComponentsPROTEIN (PERIPLASMIC IRON-BINDING PROTEIN)
KeywordsMETAL BINDING PROTEIN / FERRIC BINDING PROTEIN / PERIPLASMIC BINDING PROTEIN / FBPA / GHONNORHEA / NEISSERIA
Function / homology
Function and homology information


transmembrane transport / iron ion transport / 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 / ABC transporter periplasmic binding protein
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsMcRee, D.E. / Bruns, C.M. / Williams, P.A. / Mietzner, T.A. / Nunn, R.
CitationJournal: To be Published
Title: Structural Basis of Iron Uptake in the Pathogen Neisseria gonorrhoeae
Authors: McRee, D.E. / Bruns, C.M. / Williams, P.A. / Mietzner, T.A. / Nunn, R.
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 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: PROTEIN (PERIPLASMIC IRON-BINDING PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8553
Polymers33,7041
Non-polymers1512
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.583, 111.009, 140.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (PERIPLASMIC IRON-BINDING PROTEIN)


Mass: 33704.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GRAM-NEGATIVE HUMAN PATHOGENIC BACTERIA / Source: (natural) Neisseria gonorrhoeae (bacteria) / Strain: FBPA / References: UniProt: Q50964
#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.: 335 / 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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 10
Details: PEG 4K CAPS NASCN, pH 10, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.2→10 Å / Num. all: 14938 / Num. obs: 14938 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.297 / % possible all: 29.7

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
MAR345data collection
SCALEPACKdata scaling
RefinementResolution: 2.2→10 Å / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.377 768 RANDOM
Rwork0.231 --
all0.23 14397 -
obs0.185 11172 -
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 6 335 2756

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