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- PDB-1xc1: Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (FBP) -

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Basic information

Entry
Database: PDB / ID: 1xc1
TitleOxo Zirconium(IV) Cluster in the Ferric Binding Protein (FBP)
Componentsperiplasmic iron-binding protein
KeywordsMETAL TRANSPORT / PERIPLASMIC FERRIC BINDING PROTEIN / ZIRCONIUM / METAL-OXO CLUSTER
Function / homology
Function and homology information


transmembrane transport / iron ion 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
OXO ZIRCONIUM(IV) CLUSTER / : / Major ferric iron-binding protein
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsZhong, W. / Alexeev, D. / Harvey, I. / Guo, M. / Hunter, D.J.B. / Zhu, H. / Campopiano, D.J. / Sadler, P.J.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2004
Title: Assembly of an Oxo-Zirconium(IV) Cluster in a Protein Cleft
Authors: Zhong, W. / Alexeev, D. / Harvey, I. / Guo, M. / Hunter, D.J.B. / Zhu, H. / Campopiano, D.J. / Sadler, P.J.
#1: Journal: 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.B. / Campopiano, D.J. / Sadler, P.J.
History
DepositionAug 31, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / 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: periplasmic iron-binding protein
B: periplasmic iron-binding protein
C: periplasmic iron-binding protein
D: periplasmic iron-binding protein
E: periplasmic iron-binding protein
F: periplasmic iron-binding protein
G: periplasmic iron-binding protein
H: periplasmic iron-binding protein
I: periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)308,38518
Polymers303,1959
Non-polymers5,1909
Water17,547974
1
A: periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2652
Polymers33,6881
Non-polymers5771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2652
Polymers33,6881
Non-polymers5771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2652
Polymers33,6881
Non-polymers5771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2652
Polymers33,6881
Non-polymers5771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2652
Polymers33,6881
Non-polymers5771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2652
Polymers33,6881
Non-polymers5771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2652
Polymers33,6881
Non-polymers5771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2652
Polymers33,6881
Non-polymers5771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2652
Polymers33,6881
Non-polymers5771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.200, 146.200, 113.558
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
periplasmic iron-binding protein / Ferric binding protein / Iron transporter protein


Mass: 33688.348 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: FBPA / Plasmid: PTRC99A-FBP-NG / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: GenBank: 1098687, UniProt: P17259*PLUS
#2: Chemical
ChemComp-ZRC / OXO ZIRCONIUM(IV) CLUSTER


Mass: 576.636 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: O17PZr3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 974 / 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: 2.32 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: PEG 4000, NaCl, imidasole/malate, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 2002 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.51→20 Å / Num. all: 426023 / Num. obs: 414535 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 16.3
Reflection shellResolution: 1.51→1.58 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 1.3 / Num. unique all: 46715 / Rsym value: 0.81 / % possible all: 94.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1O7T

1o7t


Resolution: 1.51→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Twinned least squares refinement with the twinning fraction of 0.49
RfactorNum. reflection% reflectionSelection details
Rfree0.275 19016 -RANDOM
Rwork0.191 ---
obs0.191 414535 97.3 %-
all-426023 --
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.92 Å2-2.92 Å2-2.92 Å2
2---2.92 Å20 Å2
3---5.84 Å2
Refinement stepCycle: LAST / Resolution: 1.51→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21402 0 171 974 22547
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0145
X-RAY DIFFRACTIONc_angle_d2.44
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.51-1.580.3220590.32X-RAY DIFFRACTION467156
1.58-1.660.3322920.3X-RAY DIFFRACTION484676
1.66-1.770.3223930.29X-RAY DIFFRACTION491076
1.77-1.90.322640.27X-RAY DIFFRACTION496446
1.9-2.090.2823500.24X-RAY DIFFRACTION499646
2.09-2.40.326400.21X-RAY DIFFRACTION502196

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