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- PDB-1r1n: Tri-nuclear oxo-iron clusters in the ferric binding protein from ... -

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Basic information

Entry
Database: PDB / ID: 1r1n
TitleTri-nuclear oxo-iron clusters in the ferric binding protein from N. gonorrhoeae
ComponentsFerric-iron Binding Protein
KeywordsIRON BINDING PROTEIN
Function / homology
Function and homology information


transmembrane transport / iron ion transport / outer membrane-bounded 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
OXO-IRON CLUSTER 2 / OXO-IRON CLUSTER 1 / OXO-IRON CLUSTER 3 / Major ferric iron-binding protein
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsZhu, H. / Alexeev, D. / Hunter, D.J. / Campopiano, D.J. / Sadler, P.J.
CitationJournal: Biochem.J. / Year: 2003
Title: Oxo-iron clusters in a bacterial iron-trafficking protein: new roles for a conserved motif.
Authors: Zhu, H. / Alexeev, D. / Hunter, D.J. / Campopiano, D.J. / Sadler, P.J.
History
DepositionSep 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.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 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / pdbx_distant_solvent_atoms ...chem_comp_atom / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _chem_comp_atom.pdbx_stereo_config

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferric-iron Binding Protein
B: Ferric-iron Binding Protein
C: Ferric-iron Binding Protein
D: Ferric-iron Binding Protein
E: Ferric-iron Binding Protein
F: Ferric-iron Binding Protein
G: Ferric-iron Binding Protein
H: Ferric-iron Binding Protein
I: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,44418
Polymers303,1959
Non-polymers3,2499
Water50,7482817
1
A: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0402
Polymers33,6881
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0402
Polymers33,6881
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0572
Polymers33,6881
Non-polymers3691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0402
Polymers33,6881
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0572
Polymers33,6881
Non-polymers3691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0572
Polymers33,6881
Non-polymers3691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0572
Polymers33,6881
Non-polymers3691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0402
Polymers33,6881
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Ferric-iron Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0572
Polymers33,6881
Non-polymers3691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.500, 146.500, 114.969
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Ferric-iron Binding Protein


Mass: 33688.348 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Neisseria gonorrhoeae (bacteria) / References: UniProt: P17259
#2: Chemical
ChemComp-CNB / OXO-IRON CLUSTER 1


Mass: 351.592 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe3H8O11
#3: Chemical
ChemComp-CN1 / OXO-IRON CLUSTER 2


Mass: 368.599 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe3H9O12
#4: Chemical ChemComp-CNF / OXO-IRON CLUSTER 3


Mass: 368.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3H9O12
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2817 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 47.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 1450, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: multilayer osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→20 Å / Num. all: 283046 / Num. obs: 280085 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 7.1
Reflection shellResolution: 1.74→1.82 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.1 / Num. unique all: 33430 / Rsym value: 0.47 / % possible all: 87.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O7T

1o7t


Resolution: 1.74→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3 11189 -RANDOM
Rwork0.167 ---
all0.167 283046 --
obs0.167 280085 99 %-
Displacement parametersBiso mean: 44.4 Å2
Refinement stepCycle: LAST / Resolution: 1.74→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21402 0 131 2817 24350
LS refinement shellResolution: 1.74→1.82 Å
RfactorNum. reflection% reflection
Rfree0.38 1366 -
Rwork0.34 --
obs-33430 87.1 %

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