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- PDB-4y2k: reduced form of apo-GolB -

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Basic information

Entry
Database: PDB / ID: 4y2k
Titlereduced form of apo-GolB
ComponentsPutative metal-binding transport protein
KeywordsMETAL TRANSPORT / Redued 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: 1.7 Å
AuthorsWei, W. / Wang, F. / Ma, L. / Zhao, J.
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

Downloads & links

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Assembly

Deposited unit
A: Putative metal-binding transport protein


Theoretical massNumber of molelcules
Total (without water)6,9281
Polymers6,9281
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3800 Å2
Unit cell
Length a, b, c (Å)37.008, 37.008, 169.938
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
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 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 8190 / % possible obs: 97.2 % / Redundancy: 6.8 % / Net I/σ(I): 28.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 7.52 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.7→31.49 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.269 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.108
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23255 369 4.6 %RANDOM
Rwork0.20508 ---
obs0.20634 7707 96.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.837 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.7→31.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms481 0 0 56 537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019494
X-RAY DIFFRACTIONr_bond_other_d0.0060.02489
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.972670
X-RAY DIFFRACTIONr_angle_other_deg0.75131128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.14124.21119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1471588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.052154
X-RAY DIFFRACTIONr_chiral_restr0.0790.283
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021554
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_it3.2432.259261
X-RAY DIFFRACTIONr_mcbond_other3.2442.254260
X-RAY DIFFRACTIONr_mcangle_it5.0863.353325
X-RAY DIFFRACTIONr_mcangle_other5.0833.357326
X-RAY DIFFRACTIONr_scbond_it4.5882.69232
X-RAY DIFFRACTIONr_scbond_other4.5782.698233
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3163.856344
X-RAY DIFFRACTIONr_long_range_B_refined8.73918.845571
X-RAY DIFFRACTIONr_long_range_B_other8.59318.188548
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 25 -
Rwork0.304 515 -
obs--92.62 %

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