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- PDB-5f0u: Crystal structure of Gold binding protein -

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Basic information

Entry
Database: PDB / ID: 5f0u
TitleCrystal structure of Gold binding protein
ComponentsPutative copper chaperone
KeywordsMETAL BINDING PROTEIN / Silver binding protein
Function / homologyAlpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / SILVER ION / :
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Give str. S5-487 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.68 Å
AuthorsWei, W. / Wang, F. / Zhao, J.
CitationJournal: To Be Published
Title: Structure of tetrasilver bound to GolB at 1.70 Angstroms resolution
Authors: Wei, W. / Zhao, J. / Wang, F.
History
DepositionNov 28, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative copper chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4676
Polymers6,9281
Non-polymers5395
Water81145
1
A: Putative copper chaperone
hetero molecules

A: Putative copper chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,93412
Polymers13,8562
Non-polymers1,07910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2130 Å2
ΔGint-44 kcal/mol
Surface area6650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.095, 37.095, 170.032
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-242-

HOH

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Components

#1: Protein Putative copper chaperone / gold binding protein GolB


Mass: 6927.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Give str. S5-487 (bacteria)
Strain: S5-487 / Gene: LTSEGIV_0549 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G5ME98
#2: Chemical
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ag
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0 M Ammonium citrate tribasic, 0.1 M BIS-TRIS propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5419 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 8466 / % possible obs: 98 % / Redundancy: 11.6 % / Net I/σ(I): 24.31
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 3.756

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data reduction
RefinementResolution: 1.68→32.13 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.23 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22699 390 4.7 %RANDOM
Rwork0.19749 ---
obs0.19884 7910 96.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.294 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å20 Å2
2---0.03 Å20 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.68→32.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms481 0 5 45 531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.019496
X-RAY DIFFRACTIONr_bond_other_d0.0010.02488
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.972672
X-RAY DIFFRACTIONr_angle_other_deg0.80431126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.581566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00424.21119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2041588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.95154
X-RAY DIFFRACTIONr_chiral_restr0.1030.282
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021561
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02101
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3782.704264
X-RAY DIFFRACTIONr_mcbond_other3.3082.695263
X-RAY DIFFRACTIONr_mcangle_it4.9094.032330
X-RAY DIFFRACTIONr_mcangle_other4.9164.038331
X-RAY DIFFRACTIONr_scbond_it5.5183.299231
X-RAY DIFFRACTIONr_scbond_other5.5063.308232
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.5414.683342
X-RAY DIFFRACTIONr_long_range_B_refined10.20922.429557
X-RAY DIFFRACTIONr_long_range_B_other10.12121.893543
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.684→1.728 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 21 -
Rwork0.219 405 -
obs--73.32 %

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