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- PDB-4zv1: An ancestral arginine-binding protein bound to arginine -

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Basic information

Entry
Database: PDB / ID: 4zv1
TitleAn ancestral arginine-binding protein bound to arginine
ComponentsAncQR
KeywordsSOLUTE-BINDING PROTEIN / periplasmic binding protein / solute binding protein / transport / amino acid
Function / homologyARGININE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsClifton, B.E. / Carr, P.D. / 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

Downloads & links

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Assembly

Deposited unit
A: AncQR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9012
Polymers25,7261
Non-polymers1751
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.460, 60.410, 103.990
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-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Li2SO4, 0.1 M HEPES pH 7.5, 27.5% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.52→28.56 Å / Num. obs: 40887 / % possible obs: 99.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 12
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 2.4 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLM7.0.9data reduction
Aimless0.1.29data scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WDN

1wdn


Resolution: 1.52→28.56 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.261 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 2052 5 %RANDOM
Rwork0.16998 ---
obs0.17154 38763 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.732 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.52→28.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 12 308 2048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191907
X-RAY DIFFRACTIONr_bond_other_d0.0010.021913
X-RAY DIFFRACTIONr_angle_refined_deg2.3181.9762579
X-RAY DIFFRACTIONr_angle_other_deg0.93834437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3415257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1925.62580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92415369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.157156
X-RAY DIFFRACTIONr_chiral_restr0.1330.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02406
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_it1.6911.202962
X-RAY DIFFRACTIONr_mcbond_other1.6911.203961
X-RAY DIFFRACTIONr_mcangle_it2.5491.81208
X-RAY DIFFRACTIONr_mcangle_other2.5481.7991209
X-RAY DIFFRACTIONr_scbond_it2.841.433945
X-RAY DIFFRACTIONr_scbond_other2.841.434945
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3132.0091360
X-RAY DIFFRACTIONr_long_range_B_refined6.70211.1512391
X-RAY DIFFRACTIONr_long_range_B_other6.42510.182202
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 140 -
Rwork0.264 2678 -
obs--94.6 %

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