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- PDB-4pww: Crystal Structure of Engineered Protein. Northeast Structural Gen... -

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Basic information

Entry
Database: PDB / ID: 4pww
TitleCrystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR494.
ComponentsOR494
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / De Novo / OR494
Function / homologyRibosomal protein S10 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / ACETIC ACID / PHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.471 Å
AuthorsVorobiev, S. / Lin, Y.-R. / Seetharaman, J. / Xiao, R. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Engineered Protein OR494.
Authors: Vorobiev, S. / Lin, Y.-R. / Seetharaman, J. / Xiao, R. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMar 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Sep 20, 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 / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OR494
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4665
Polymers10,1911
Non-polymers2754
Water1,72996
1
A: OR494
hetero molecules

A: OR494
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,93210
Polymers20,3812
Non-polymers5508
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_566x,-y+1,-z+3/21
Buried area2360 Å2
ΔGint-22 kcal/mol
Surface area8920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.548, 69.645, 73.138
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

21A-571-

HOH

31A-593-

HOH

Detailsdimer as reported by HPLC+light scattering

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Components

#1: Protein OR494


Mass: 10190.724 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: OR494-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 291 K / Method: microbatch crystallization under oil / pH: 3.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: 2.0M ammonium sulfate, 0.1M citric acid, pH 3.5, Microbatch crystallization under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97907 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 14, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. all: 28181 / Num. obs: 27476 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 16.38 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 33.25
Reflection shellResolution: 1.47→1.52 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2840 / % possible all: 91.2

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KY3

4ky3


Resolution: 1.471→36.569 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 22.04 / Stereochemistry target values: ML
Details: Presence of phosphate and acetate ions were traced back to a purification procedure. There is unknown ligand in the structure which was modeled by water molecules (A593-596).
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1390 5.06 %RANDOM
Rwork0.179 ---
obs0.181 27452 97.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.118 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso max: 64.69 Å2 / Biso mean: 25.281 Å2 / Biso min: 11 Å2
Baniso -1Baniso -2Baniso -3
1--3.685 Å20 Å2-0 Å2
2--9.324 Å2-0 Å2
3----5.639 Å2
Refinement stepCycle: LAST / Resolution: 1.471→36.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms674 0 17 96 787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006694
X-RAY DIFFRACTIONf_angle_d0.936927
X-RAY DIFFRACTIONf_chiral_restr0.057106
X-RAY DIFFRACTIONf_plane_restr0.003119
X-RAY DIFFRACTIONf_dihedral_angle_d11.54263
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.471-1.5230.3251360.2722458259492
1.523-1.5840.2181390.1952565270496
1.584-1.6560.2831750.1882579275497
1.656-1.7430.2561390.1732559269897
1.743-1.8530.2471400.1692609274997
1.853-1.9960.2131120.1662653276598
1.996-2.1970.1881530.162635278899
2.197-2.5140.1891420.1532633277599
2.514-3.1680.2121290.1812668279799
3.168-36.580.2111250.18927032828100

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