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

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Basic information

Entry
Database: PDB / ID: 4hqd
TitleCrystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR265.
ComponentsEngineered Protein OR265
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Engineered Protein / Northeast Structural Genomics Consortium / NESG
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.433 Å
AuthorsVorobiev, S. / Su, M. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / Maglaqui, M. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. ...Vorobiev, S. / Su, M. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / Maglaqui, M. / Xiao, R. / Lee, D. / 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 OR265.
Authors: Vorobiev, S. / Su, M. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / Maglaqui, M. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Engineered Protein OR265
B: Engineered Protein OR265


Theoretical massNumber of molelcules
Total (without water)37,0572
Polymers37,0572
Non-polymers00
Water1,45981
1
A: Engineered Protein OR265


Theoretical massNumber of molelcules
Total (without water)18,5291
Polymers18,5291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Engineered Protein OR265


Theoretical massNumber of molelcules
Total (without water)18,5291
Polymers18,5291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.004, 30.461, 70.061
Angle α, β, γ (deg.)90.000, 92.680, 90.000
Int Tables number4
Space group name H-MP1211
Detailsmonomer,17.1 kD,98.1%

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Components

#1: Protein Engineered Protein OR265


Mass: 18528.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: Engineered protein / Plasmid: pET21_NESG, OR265-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 1.98 Å3/Da / Density % sol: 38.03 %
Crystal growTemperature: 277 K / Method: microbatch crystallization under oil / pH: 7.5
Details: 40% PEG 400, 0.1M lithium sulfate, 0.1M HEPES, pH 7.5, Microbatch crystallization under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97905 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 11, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. all: 21255 / Num. obs: 20809 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 31.32 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 17.6
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 4.34 / Num. unique all: 2149 / % possible all: 95.1

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 4HB5

4hb5


Resolution: 2.433→34.992 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.72 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.227 990 4.76 %RANDOM
Rwork0.197 ---
obs0.199 20800 97.25 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.349 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 119.2 Å2 / Biso mean: 41.067 Å2 / Biso min: 5.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.83 Å2-0 Å2-7.366 Å2
2---1.56 Å20 Å2
3---8.39 Å2
Refinement stepCycle: LAST / Resolution: 2.433→34.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 0 81 2523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062471
X-RAY DIFFRACTIONf_angle_d1.1693316
X-RAY DIFFRACTIONf_chiral_restr0.087368
X-RAY DIFFRACTIONf_plane_restr0.005438
X-RAY DIFFRACTIONf_dihedral_angle_d14.339946
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.433-2.5620.291320.2592658279091
2.562-2.7220.2941660.2262867303399
2.722-2.9320.2781370.2142839297699
2.932-3.2270.3021420.2072849299198
3.227-3.6930.2031330.192879301298
3.693-4.6520.1881490.1812828297798
4.652-34.9960.191310.1792890302199
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)
10.00180.0003-0.00110.0009-0.0020.00290.04490.0025-0.0065-0.0069-0.04540.0199-0.01410.013-00.049-0.028-0.1207-0.0113-0.0618-0.015225.21780.51066.2982
20.00270.0001-0-0.0004-0.00080.0051-0.0173-0.0046-0.0021-0.001-0.00390.0068-0.0037-0.003300.03970.00420.01650.07980.0190.07718.2902-6.7216-27.1113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 164
2X-RAY DIFFRACTION2chain BB2 - 161

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