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- PDB-4y2i: Gold ion bound to GolB -

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Basic information

Entry
Database: PDB / ID: 4y2i
TitleGold ion bound to GolB
ComponentsPutative metal-binding transport protein
KeywordsMETAL TRANSPORT / Gold binding protein
Function / homology
Function and homology information


Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Putative metal-binding transport protein / :
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsWei, W. / Wang, F. / Ma, L. / Zhao, J.
Funding support China, 3items
OrganizationGrant numberCountry
the National Science Foundation of China21332005 China
the MOST of China2014AA020512 China
the National Natural Science Foundation of China31200607 China
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Structural Insights and the Surprisingly Low Mechanical Stability of the Au-S Bond in the Gold-Specific Protein GolB
Authors: Wei, W. / Sun, Y. / Zhu, M. / Liu, X. / Sun, P. / Wang, F. / Gui, Q. / Meng, W. / Cao, Y. / Zhao, J.
History
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative metal-binding transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3223
Polymers6,9281
Non-polymers3942
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-9 kcal/mol
Surface area3850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.093, 37.093, 169.911
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Putative metal-binding transport 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 Typhimurium (bacteria)
Strain: DT2 / Gene: STMDT2_03511 / Production host: Escherichia coli (E. coli) / References: UniProt: U4MDP1, UniProt: A0A140UHB4*PLUS
#2: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Au
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 49.49 %
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: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 7169 / % possible obs: 99 % / Redundancy: 10.6 % / Net I/σ(I): 51
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.2 / % possible all: 86.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2→31.56 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.889 / SU B: 3.623 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26638 240 4.6 %RANDOM
Rwork0.22678 ---
obs0.22867 5003 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2--0.87 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2→31.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms481 0 2 34 517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.019494
X-RAY DIFFRACTIONr_bond_other_d0.0010.02501
X-RAY DIFFRACTIONr_angle_refined_deg0.8531.972670
X-RAY DIFFRACTIONr_angle_other_deg0.51531140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.596566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14124.21119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5341588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.542154
X-RAY DIFFRACTIONr_chiral_restr0.0470.283
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021554
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02100
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_it2.5762.07261
X-RAY DIFFRACTIONr_mcbond_other2.5792.063260
X-RAY DIFFRACTIONr_mcangle_it4.0973.073325
X-RAY DIFFRACTIONr_mcangle_other4.0943.079326
X-RAY DIFFRACTIONr_scbond_it3.8312.53233
X-RAY DIFFRACTIONr_scbond_other3.8232.538234
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9283.571344
X-RAY DIFFRACTIONr_long_range_B_refined8.75116.612539
X-RAY DIFFRACTIONr_long_range_B_other8.74816.454533
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 15 -
Rwork0.284 360 -
obs--98.43 %

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