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- PDB-4ney: Crystal Structure of an engineered protein with ferredoxin fold, ... -

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Basic information

Entry
Database: PDB / ID: 4ney
TitleCrystal Structure of an engineered protein with ferredoxin fold, Northeast Structural Genomics Consortium (NESG) Target OR277
ComponentsEngineered protein OR277
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / ferredoxin fold / protein engineering / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyRibosomal protein S10 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / tetrabutylphosphonium
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.323 Å
AuthorsGuan, R. / Lin, Y.-R. / Koga, N. / Koga, R. / Castellanos, J. / Seetharaman, J. / Maglaqui, M. / Sahdev, S. / Mao, L. / Xiao, R. ...Guan, R. / Lin, Y.-R. / Koga, N. / Koga, R. / Castellanos, J. / Seetharaman, J. / Maglaqui, M. / Sahdev, S. / Mao, L. / Xiao, R. / Everett, J.K. / Baker, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be published
Title: Northeast Structural Genomics Consortium Target OR277
Authors: Guan, R. / Lin, Y.-R. / Koga, N. / Koga, R. / Castellanos, J. / Seetharaman, J. / Maglaqui, M. / Sahdev, S. / Mao, L. / Xiao, R. / Everett, J.K. / Baker, D. / Montelione, G.T.
History
DepositionOct 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Engineered protein OR277
B: Engineered protein OR277
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2944
Polymers40,9122
Non-polymers3822
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3487.5 Å2
ΔGint-1 kcal/mol
Surface area17601.5 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.282, 79.289, 97.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain B and segidB0
Detailsdimer,39.48 kD,98.5%

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Components

#1: Protein Engineered protein OR277


Mass: 20456.123 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This is a designed protein. / Source: (synth.) artificial gene (others)
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-4NE / tetrabutylphosphonium


Mass: 259.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H36P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Protein solution - 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution - 25% PEG 3350, 5% w/v Tetrabutylphosphonium bromide, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97924 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 28, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. all: 15080 / Num. obs: 15080 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.1 % / Biso Wilson estimate: 38.82 Å2 / Rmerge(I) obs: 0.069
Reflection shellResolution: 2.32→2.36 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 7.08 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.323→39.645 Å / Occupancy max: 1 / Occupancy min: 0.6 / SU ML: 0.27 / σ(F): 0 / Phase error: 25.8 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2599 1473 9.96 %
Rwork0.2159 --
obs0.2201 14793 97.97 %
all-15038 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.94 Å2
Refinement stepCycle: LAST / Resolution: 2.323→39.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 25 129 2948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042858
X-RAY DIFFRACTIONf_angle_d0.8523812
X-RAY DIFFRACTIONf_dihedral_angle_d13.2991125
X-RAY DIFFRACTIONf_chiral_restr0.034401
X-RAY DIFFRACTIONf_plane_restr0.003492
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1486X-RAY DIFFRACTIONTORSIONAL12.402
12B1486X-RAY DIFFRACTIONTORSIONAL12.402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.323-2.3980.28961170.27021065X-RAY DIFFRACTION89
2.398-2.48370.32771300.24211183X-RAY DIFFRACTION98
2.4837-2.58310.31071350.24341203X-RAY DIFFRACTION99
2.5831-2.70060.27151340.24711201X-RAY DIFFRACTION99
2.7006-2.8430.29261330.24651210X-RAY DIFFRACTION99
2.843-3.0210.30081360.25751222X-RAY DIFFRACTION100
3.021-3.25420.26351340.23431226X-RAY DIFFRACTION100
3.2542-3.58150.25751320.22071221X-RAY DIFFRACTION99
3.5815-4.09930.27521380.19811240X-RAY DIFFRACTION99
4.0993-5.16280.19751390.18021257X-RAY DIFFRACTION100
5.1628-39.65030.25061450.20511292X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7228-0.4335-0.08750.95840.40071.6176-0.2602-0.1520.1982-0.03940.0536-0.2511-0.8073-0.326-0.03950.2295-0.0363-0.04420.1181-0.00260.211128.446746.361966.7763
20.8636-0.28651.51462.4179-1.30492.44160.1321-0.0805-0.1745-0.51860.12050.3350.607-0.15170.32360.30350.0076-0.02360.1522-0.01330.23122.023931.077164.8447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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