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- PDB-1o7t: Metal nanoclusters bound to the Ferric Binding Protein from Neiss... -

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Basic information

Entry
Database: PDB / ID: 1o7t
TitleMetal nanoclusters bound to the Ferric Binding Protein from Neisseria gonorrhoeae.
ComponentsIRON BINDING PROTEINIron-binding proteins
KeywordsMETAL BINDING PROTEIN / METAL-BINDING PROTEIN / PERIPLASMIC FERRIC BINDING PROTEIN / HAFNIUM / METAL-OXO CLUSTER
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
SMALLEST HF-OXO-PHOSPHATE CLUSTER HF3 / HF OXO CLUSTER HF5 / HF-OXO-PHOSPHATE CLUSTER PHF / ABC transporter periplasmic binding protein
Similarity search - Component
Biological speciesNEISSERIA GONORRHOEAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAlexeev, D. / Zu, H. / Guo, M. / Zhong, W. / Hunter, D.J.B. / Yang, W. / Campopiano, D.J. / Sadler, P.J.
CitationJournal: Nat. Struct. Biol. / Year: 2003
Title: A novel protein-mineral interface.
Authors: Alexeev, D. / Zhu, H. / Guo, M. / Zhong, W. / Hunter, D.J. / Yang, W. / Campopiano, D.J. / Sadler, P.J.
History
DepositionNov 12, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / citation_author / exptl_crystal_grow
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IRON BINDING PROTEIN
B: IRON BINDING PROTEIN
C: IRON BINDING PROTEIN
D: IRON BINDING PROTEIN
E: IRON BINDING PROTEIN
F: IRON BINDING PROTEIN
G: IRON BINDING PROTEIN
H: IRON BINDING PROTEIN
I: IRON BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,99318
Polymers303,0699
Non-polymers10,9249
Water35,5981976
1
A: IRON BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9152
Polymers33,6741
Non-polymers1,2411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: IRON BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9152
Polymers33,6741
Non-polymers1,2411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: IRON BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9152
Polymers33,6741
Non-polymers1,2411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: IRON BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4882
Polymers33,6741
Non-polymers8131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: IRON BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9152
Polymers33,6741
Non-polymers1,2411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: IRON BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9152
Polymers33,6741
Non-polymers1,2411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
G: IRON BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9772
Polymers33,6741
Non-polymers1,3021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
H: IRON BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9772
Polymers33,6741
Non-polymers1,3021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
9
I: IRON BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9772
Polymers33,6741
Non-polymers1,3021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)148.128, 148.128, 115.842
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99883, -0.04815, -0.00371), (0.04818, 0.9988, 0.00887), (0.00328, -0.00904, 0.99995)-71.20693, -46.93589, 0.42112
2given(0.99989, 0.01353, -0.0056), (-0.01353, 0.99991, 0.0002), (0.0056, -0.00012, 0.99998)2.42088, -86.21367, -0.08817
3given(0.52169, 0.85313, 0.00027), (0.85308, -0.52166, 0.01145), (0.00991, -0.00574, -0.99993)-1.15895, 5.60345, 0.91863
4given(0.53878, 0.84244, -0.0036), (0.84245, -0.53878, 0.0021), (-0.00017, -0.00417, -0.99999)-72.75784, -39.32858, 1.08629
5given(0.53699, 0.84357, 0.00546), (0.84358, -0.53701, 0.00058), (0.00342, 0.0043, -0.99998)-75.69582, 45.88309, 0.58551
6given(0.18435, -0.98243, -0.02901), (0.98284, 0.18409, 0.01136), (-0.00582, -0.03061, 0.99951)38.17521, -31.54342, 24.42211
7given(0.28976, -0.957, -0.01396), (0.95693, 0.2894, 0.02286), (-0.01784, -0.01998, 0.99964)108.69543, 7.35772, 23.2842
8given(0.96044, -0.27811, 0.01472), (-0.27757, -0.96021, -0.03077), (0.0227, 0.02546, -0.99942)-11.13714, 133.67616, -22.94109

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Components

#1: Protein
IRON BINDING PROTEIN / Iron-binding proteins


Mass: 33674.320 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA GONORRHOEAE (bacteria) / Strain: FBPA / Plasmid: PTRC99A/FBP/NG / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): TOP10 / References: UniProt: Q50964
#2: Chemical
ChemComp-HF5 / HF OXO CLUSTER HF5


Mass: 1240.533 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: H12Hf5O21
#3: Chemical ChemComp-HF3 / SMALLEST HF-OXO-PHOSPHATE CLUSTER HF3


Mass: 813.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H7Hf3O15P
#4: Chemical ChemComp-PHF / HF-OXO-PHOSPHATE CLUSTER PHF


Mass: 1302.497 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H11Hf5O23P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1976 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsHF5 - HFC LINKED TO OH OF TYR195 HF5 - HFA LINKED TO OH OF TYR196 HF3 - HFC LINKED TO OH OF TYR195 ...HF5 - HFC LINKED TO OH OF TYR195 HF5 - HFA LINKED TO OH OF TYR196 HF3 - HFC LINKED TO OH OF TYR195 HF3 - HFA LINKED TO OH OF TYR196 PHOSPHATE BRIDGES HFA-HFB-HFC PHF - HFC LINKED TO OH OF TYR195 PHF - HFA LINKED TO OH OF TYR196 PHOSPHATE BRIDGES HFA-HFD-HFE

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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: 1.94 Å3/Da / Density % sol: 36.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 4MG/ML PROTEIN IN 4MM PHOSPHATE, 25MM NAHCO3 PLUS 20% PEG 4000, 0.2M KCL, 0.4M IMIDAZOLE/MALATE BUFFER PH7.7, pH 7.40
Crystal grow
*PLUS
Temperature: 290 K / pH: 7.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 %(w/v)PEG40001reservoir
20.2 M1reservoirKCl
30.4 Mimidazole-malate1reservoirpH7.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 2001 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 406392 / % possible obs: 100 % / Redundancy: 8.4 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 1.8 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 100 % / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D9Y

1d9y


Resolution: 1.65→30 Å / Data cutoff high absF: 100000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 23837 7 %RANDOM
Rwork0.1642 ---
obs0.1642 341561 100 %-
Solvent computationSolvent model: FLAT / Bsol: 54 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.474 Å2-3.028 Å20 Å2
2---3.474 Å20 Å2
3---6.949 Å2
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21393 0 236 1976 23605
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.264 / Rfactor Rwork: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.24

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