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- PDB-4zv2: An ancestral arginine-binding protein bound to glutamine -

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Basic information

Entry
Database: PDB / ID: 4zv2
TitleAn ancestral arginine-binding protein bound to glutamine
ComponentsAncQR
KeywordsSOLUTE-BINDING PROTEIN / periplasmic binding protein / solute binding protein / transport / amino acid
Function / homologyGLUTAMINE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsClifton, B.E. / Jackson, C.J.
CitationJournal: Cell Chem Biol / Year: 2016
Title: Ancestral Protein Reconstruction Yields Insights into Adaptive Evolution of Binding Specificity in Solute-Binding Proteins.
Authors: Clifton, B.E. / Jackson, C.J.
History
DepositionMay 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Sep 27, 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 / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AncQR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8722
Polymers25,7261
Non-polymers1461
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.200, 61.300, 104.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AncQR


Mass: 25725.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pETMCSIII / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M MgCl2, 0.1 M HEPES pH 7.5, 24% (w/v) PEG 3350, microseeds from crushed crystals produced using same precipitant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9655 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.43→36.2 Å / Num. obs: 43838 / % possible obs: 99.7 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.178 / Net I/σ(I): 9.2
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.871 / Mean I/σ(I) obs: 1.5 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
Aimless0.1.29data scaling
MOSFLM7.0.9data reduction
MOLREP11.1.00phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZV1

4zv1


Resolution: 1.43→34.21 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.072 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20487 2193 5 %RANDOM
Rwork0.18175 ---
obs0.18293 41372 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.311 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.43→34.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 10 266 1996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0191809
X-RAY DIFFRACTIONr_bond_other_d0.0010.021804
X-RAY DIFFRACTIONr_angle_refined_deg2.2991.9752442
X-RAY DIFFRACTIONr_angle_other_deg134181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2935241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95725.92176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65115345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.745155
X-RAY DIFFRACTIONr_chiral_restr0.1590.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022051
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02378
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_it1.6461.307919
X-RAY DIFFRACTIONr_mcbond_other1.6471.308918
X-RAY DIFFRACTIONr_mcangle_it2.4531.9531148
X-RAY DIFFRACTIONr_mcangle_other2.4521.9521149
X-RAY DIFFRACTIONr_scbond_it2.6741.518890
X-RAY DIFFRACTIONr_scbond_other2.6741.518890
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0332.1611286
X-RAY DIFFRACTIONr_long_range_B_refined5.46311.4382252
X-RAY DIFFRACTIONr_long_range_B_other5.40210.7892108
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.43→1.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 142 -
Rwork0.286 2900 -
obs--95.42 %

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