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- PDB-3mfq: A Glance into the Metal Binding Specificity of TroA: Where Elabor... -

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Basic information

Entry
Database: PDB / ID: 3mfq
TitleA Glance into the Metal Binding Specificity of TroA: Where Elaborate Behaviors Occur in the Active Center
ComponentsHigh-affinity zinc uptake system protein znuA
KeywordsMETAL BINDING PROTEIN / TroA
Function / homology
Function and homology information


metal ion transport / cell adhesion / metal ion binding
Similarity search - Function
Adhesin B / Adhesion lipoprotein / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
High-affinity zinc uptake system protein znuA
Similarity search - Component
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.598 Å
AuthorsGao, G.F. / Zheng, B. / Zhang, Q. / Gao, J. / Han, H. / Li, M.
CitationJournal: Plos One / Year: 2011
Title: Insight into the interaction of metal ions with TroA from Streptococcus suis
Authors: Zheng, B. / Zhang, Q. / Gao, J. / Han, H. / Li, M. / Zhang, J. / Qi, J. / Yan, J. / Gao, G.F.
History
DepositionApr 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Nov 1, 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_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_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_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_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_label_asym_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: High-affinity zinc uptake system protein znuA
B: High-affinity zinc uptake system protein znuA
C: High-affinity zinc uptake system protein znuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8936
Polymers94,6973
Non-polymers1963
Water4,396244
1
A: High-affinity zinc uptake system protein znuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6312
Polymers31,5661
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: High-affinity zinc uptake system protein znuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6312
Polymers31,5661
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: High-affinity zinc uptake system protein znuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6312
Polymers31,5661
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.360, 102.360, 107.333
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein High-affinity zinc uptake system protein znuA / TroA


Mass: 31565.549 Da / Num. of mol.: 3 / Fragment: residues in UNP 36-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Strain: 05ZYH33 / Gene: SSU05_2086 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A4VY63
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.1M Ammonium Sulfate, 6%(v/v) iso-propanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.502
ReflectionResolution: 2.598→50 Å / Num. obs: 30968 / Rmerge(I) obs: 0.0845
Reflection shellResolution: 2.598→2.69 Å / Rmerge(I) obs: 0.0845 / Num. unique all: 14663 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1k0f

1k0f


Resolution: 2.598→25.443 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.798 / σ(F): 0.08 / Phase error: 27.15 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1636 5.28 %random
Rwork0.226 29337 --
obs0.232 30968 90.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.567 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso max: 435.66 Å2 / Biso mean: 58.093 Å2 / Biso min: 12.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.179 Å20 Å20 Å2
2--0.179 Å2-0 Å2
3----0.358 Å2
Refinement stepCycle: LAST / Resolution: 2.598→25.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6579 0 3 244 6826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036711
X-RAY DIFFRACTIONf_angle_d0.619084
X-RAY DIFFRACTIONf_chiral_restr0.0441023
X-RAY DIFFRACTIONf_plane_restr0.0021173
X-RAY DIFFRACTIONf_dihedral_angle_d17.0072460
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.602-2.6860.3661340.4182501263581
2.686-2.7820.3651480.3482534268283
2.782-2.8930.3581410.3292557269884
2.893-3.0240.2791430.3012632277585
3.024-3.1830.2911570.2692629278686
3.183-3.3820.2531410.2472707284888
3.382-3.6420.2391380.2152736287489
3.642-4.0060.2371420.1942725286787
4.006-4.5810.2111340.1832633276786
4.581-5.7520.261430.1862791293490
5.752-21.0540.2521590.212892305192
Refinement TLS params.Method: refined / Origin x: 23.4849 Å / Origin y: -31.3634 Å / Origin z: -9.9225 Å
111213212223313233
T0.0606 Å20.0016 Å2-0.0102 Å2-0.1117 Å20.0158 Å2--0.1043 Å2
L0.1144 °2-0.009 °2-0.0251 °2-0.2218 °20.061 °2--0.079 °2
S-0.0205 Å °-0.0593 Å °-0.004 Å °-0.0171 Å °0.0038 Å °-0.0028 Å °0.0235 Å °0.0704 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA32 - 309
2X-RAY DIFFRACTION1allB32 - 309
3X-RAY DIFFRACTION1allC32 - 309
4X-RAY DIFFRACTION1allA401
5X-RAY DIFFRACTION1allB401
6X-RAY DIFFRACTION1allC401
7X-RAY DIFFRACTION1allA - B1 - 409

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