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

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Basic information

Entry
Database: PDB / ID: 4nez
TitleCrystal Structure of an engineered protein with ferredoxin fold, Northeast Structural Genomics Consortium (NESG) Target OR276
ComponentsEngineered protein OR276
KeywordsDE NOVO PROTEIN / protein engineering / ferredoxin fold / structural Genomics / PSI-Biology / 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: 2.395 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 OR276
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. / Northeast ...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. / Northeast Structural Genomics Consortium (NESG)
History
DepositionOct 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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

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Assembly

Deposited unit
A: Engineered protein OR276
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7513
Polymers20,3691
Non-polymers3822
Water36020
1
A: Engineered protein OR276
hetero molecules

A: Engineered protein OR276
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5016
Polymers40,7382
Non-polymers7634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2640 Å2
ΔGint-2 kcal/mol
Surface area16630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.834, 71.073, 109.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-201-

TRS

21A-202-

4NE

31A-301-

HOH

41A-308-

HOH

51A-320-

HOH

Detailsdimer,38.91 kD,97.8%

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Components

#1: Protein Engineered protein OR276


Mass: 20369.045 Da / Num. of mol.: 1 / 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.: 20 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
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, 0.1 M Hepes pH 7.4, 5% w/v Tetrabutylphosphonium bromide, VAPOR DIFFUSION, ...Details: Protein solution - 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution - 25% PEG 3350, 0.1 M Hepes pH 7.4, 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: 2.39→50 Å / Num. all: 8323 / Num. obs: 8240 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.9 % / Biso Wilson estimate: 64.93 Å2 / Rmerge(I) obs: 0.076
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.516 / % possible all: 96.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: SAD / Resolution: 2.395→27.566 Å / Occupancy max: 1 / Occupancy min: 0.46 / SU ML: 0.29 / σ(F): 0 / Phase error: 28.9 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2428 815 10.05 %
Rwork0.2184 --
obs0.2209 8106 97.8 %
all-8219 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.992 Å2
Refinement stepCycle: LAST / Resolution: 2.395→27.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 25 20 1339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021332
X-RAY DIFFRACTIONf_angle_d0.4871773
X-RAY DIFFRACTIONf_dihedral_angle_d11.586536
X-RAY DIFFRACTIONf_chiral_restr0.041187
X-RAY DIFFRACTIONf_plane_restr0.001227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3953-2.54530.37031300.34281161X-RAY DIFFRACTION96
2.5453-2.74170.34821330.31891213X-RAY DIFFRACTION97
2.7417-3.01730.29151340.29711182X-RAY DIFFRACTION98
3.0173-3.45310.25171390.24821232X-RAY DIFFRACTION99
3.4531-4.34780.27521390.20231244X-RAY DIFFRACTION99
4.3478-27.56780.18841400.1821259X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 7.7953 Å / Origin y: 40.7593 Å / Origin z: 30.5393 Å
111213212223313233
T0.262 Å2-0.0817 Å20.013 Å2-0.4656 Å2-0.0494 Å2--0.5462 Å2
L1.5082 °2-0.6779 °20.1314 °2-3.5917 °22.2683 °2--2.9349 °2
S-0.27 Å °-0.0989 Å °0.1707 Å °0.491 Å °0.5158 Å °-0.8918 Å °-0.3697 Å °0.4614 Å °0.3534 Å °
Refinement TLS groupSelection details: chain A

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