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Basic information

Entry
Database: PDB / ID: 4rv1
TitleCrystal Structure of Engineered Protein. Northeast Structural Genomics Consortium (NESG) Target OR497.
ComponentsEngineered Protein OR497
KeywordsDE NOVO PROTEIN / STRUCTURAL GENOMICS / PSI-BIOLOGY / PROTEIN STRUCTURE INITIATIVE / ENGINEERED PROTEIN / NESG / OR497 / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM
Function / homologyLeucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha / ACETATE ION
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.573 Å
AuthorsVorobiev, S. / Parmeggiani, F. / 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 OR497.
Authors: Vorobiev, S. / Parmeggiani, F. / Seetharaman, J. / Xiao, R. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionNov 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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

Downloads & links

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Assembly

Deposited unit
A: Engineered Protein OR497
B: Engineered Protein OR497
C: Engineered Protein OR497
D: Engineered Protein OR497
E: Engineered Protein OR497
F: Engineered Protein OR497
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,6228
Polymers257,5046
Non-polymers1182
Water8,989499
1
A: Engineered Protein OR497
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9762
Polymers42,9171
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Engineered Protein OR497


Theoretical massNumber of molelcules
Total (without water)42,9171
Polymers42,9171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Engineered Protein OR497
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9762
Polymers42,9171
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Engineered Protein OR497


Theoretical massNumber of molelcules
Total (without water)42,9171
Polymers42,9171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Engineered Protein OR497


Theoretical massNumber of molelcules
Total (without water)42,9171
Polymers42,9171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Engineered Protein OR497


Theoretical massNumber of molelcules
Total (without water)42,9171
Polymers42,9171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.265, 99.265, 432.183
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Detailsmonomer,42.25 kD,91.7%

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Components

#1: Protein
Engineered Protein OR497


Mass: 42917.348 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Gene: ARTIFICIAL GENE / Plasmid: PET21_NESG, OR497-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 291 K / Method: microbatch under paraffin oil / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 40% PEG 400, 0.1M calcium acetate, 0.1M sodium acetate, 3% ethylene glycol , microbatch under ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 40% PEG 400, 0.1M calcium acetate, 0.1M sodium acetate, 3% ethylene glycol , microbatch under paraffin 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: Jun 9, 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: 2.57→50 Å / Num. all: 151143 / Num. obs: 148422 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 55.48 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 15.2
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 2.01 / Num. unique all: 15055 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.9_1692refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 4HXT

4hxt


Resolution: 2.573→48.02 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.237 7384 5.01 %RANDOM
Rwork0.201 ---
obs0.203 147337 97.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.1 Å2 / Biso mean: 78.135 Å2 / Biso min: 21.51 Å2
Refinement stepCycle: LAST / Resolution: 2.573→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17608 0 8 499 18115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00617674
X-RAY DIFFRACTIONf_angle_d1.07323986
X-RAY DIFFRACTIONf_chiral_restr0.0773128
X-RAY DIFFRACTIONf_plane_restr0.0033116
X-RAY DIFFRACTIONf_dihedral_angle_d15.6156474
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.573-2.6020.3082810.2694596487797
2.602-2.6330.3092490.27347164965100
2.633-2.6650.3642540.3184730498499
2.665-2.6990.3972680.31447935061100
2.699-2.7340.3052280.26248015029100
2.734-2.7720.3132150.26448345049100
2.772-2.8110.3112560.26147214977100
2.811-2.8530.2722450.23448295074100
2.853-2.8980.2632270.22547624989100
2.898-2.9450.3032310.23748055036100
2.945-2.9960.272330.22948745107100
2.996-3.0510.2762420.23347514993100
3.051-3.1090.2592480.23547875035100
3.109-3.1730.3042970.24647275024100
3.173-3.2420.2922690.24648015070100
3.242-3.3170.2832770.24747665043100
3.317-3.40.2262660.2364663492998
3.4-3.4920.3082500.2264590484097
3.492-3.5950.2492640.2174766503099
3.595-3.7110.3831680.3543267343568
3.711-3.8430.262260.2064697492397
3.843-3.9970.3051990.2494024422383
3.997-4.1790.1912540.15947344988100
4.179-4.3990.1962170.15247875004100
4.399-4.6740.1872230.1548005023100
4.674-5.0350.1662430.15148185061100
5.035-5.5410.2063180.16147435061100
5.541-6.3410.2152490.17947484997100
6.341-7.9840.1592820.13947235005100
7.984-48.0290.1532050.1554300450589
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)
10.66710.1556-0.48430.2005-0.22031.6229-0.0387-0.01020.00210.0393-0.0067-0.0203-0.02010.1326-0.00010.23950.0051-0.00640.23570.0130.307444.3778-22.81416.484
20.934-0.286-0.68060.4350.27741.0209-0.0133-0.01730.06410.10070.0095-0.0649-0.05480.016800.32030.0539-0.03420.25110.02320.25880.54554.523628.5209
30.1862-0.01480.01450.4560.4261.2182-0.0454-0.00560.033-0.004-0.014-0.0137-0.07330.0802-00.29860.0282-0.01960.27780.03010.26815.1955-3.14942.5538
40.6916-0.03850.20650.7338-0.54330.90980.03880.0482-0.1520.0197-0.0610.02880.07660.0428-0.00030.2701-0.00230.02490.2032-0.01270.316242.1806-31.45122.1032
50.66210.2938-0.09321.13350.01132.722-0.1033-0.0017-0.0512-0.25310.09260.284-0.01090.1376-00.70730.03740.00180.5898-0.09990.631144.0073-27.6654-56.5909
61.627-0.18090.22020.78750.26362.19310.0686-0.1527-0.26710.140.13420.16740.12040.44530.00070.78110.0755-0.03090.7074-0.11340.633750.4286-35.4097-68.8958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 413
2X-RAY DIFFRACTION2chain BB2 - 415
3X-RAY DIFFRACTION3chain CC1 - 412
4X-RAY DIFFRACTION4chain DD1 - 415
5X-RAY DIFFRACTION5chain EE1 - 412
6X-RAY DIFFRACTION6chain FF1 - 411

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