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- PDB-4y2m: apo-GolB protein -

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Basic information

Entry
Database: PDB / ID: 4y2m
Titleapo-GolB protein
ComponentsPutative metal-binding transport protein
KeywordsMETAL TRANSPORT / Oxidized form / 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 / Resolution: 1.4 Å
AuthorsWei, W. / Zhao, J. / Wang, F.
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 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,1252
Polymers6,9281
Non-polymers1971
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-4 kcal/mol
Surface area3900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.993, 36.993, 169.761
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-18-

LYS

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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.: 1 / Source method: obtained synthetically / Formula: Au
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.17 %
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: Feb 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 22949 / % possible obs: 99.1 % / Redundancy: 9.64 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.25

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.4→31.48 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.683 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.012 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19798 1390 10 %RANDOM
Rwork0.1756 ---
obs0.17785 12504 95.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.106 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.4→31.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms481 0 1 63 545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0440.019494
X-RAY DIFFRACTIONr_bond_other_d0.0030.02487
X-RAY DIFFRACTIONr_angle_refined_deg2.0381.973670
X-RAY DIFFRACTIONr_angle_other_deg0.81931124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.541566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09324.21119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5451588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.408154
X-RAY DIFFRACTIONr_chiral_restr0.1430.282
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021554
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02100
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_it2.6081.944261
X-RAY DIFFRACTIONr_mcbond_other2.5471.934260
X-RAY DIFFRACTIONr_mcangle_it3.7272.898325
X-RAY DIFFRACTIONr_mcangle_other3.732.906326
X-RAY DIFFRACTIONr_scbond_it4.9822.398232
X-RAY DIFFRACTIONr_scbond_other4.9712.398233
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4993.387344
X-RAY DIFFRACTIONr_long_range_B_refined9.0617.394576
X-RAY DIFFRACTIONr_long_range_B_other8.73216.233545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 55 -
Rwork0.229 483 -
obs--51.78 %

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