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- PDB-6egl: Crystal Structure of a de Novo Three-stranded Coiled Coil Peptide... -

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Basic information

Entry
Database: PDB / ID: 6egl
TitleCrystal Structure of a de Novo Three-stranded Coiled Coil Peptide Containing a D-Leu in the Second Coordination Sphere of a Non-metalated Tris-thiolate Binding Site
ComponentsApo-(GRAND CoilSerL12(DLE)L16C)3
KeywordsDE NOVO PROTEIN / De Novo Three-stranded Coiled Coil Peptide / Tris-thiolate Binding Site / Engineered Protein by D-amino acids / D-Leu
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsRuckthong, L. / Stuckey, J.A. / Pecoraro, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01ES012236 United States
CitationJournal: Chemistry / Year: 2019
Title: How Outer Coordination Sphere Modifications Can Impact Metal Structures in Proteins: A Crystallographic Evaluation.
Authors: Ruckthong, L. / Stuckey, J.A. / Pecoraro, V.L.
History
DepositionAug 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.title ..._citation.journal_id_ISSN / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apo-(GRAND CoilSerL12(DLE)L16C)3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7103
Polymers4,1151
Non-polymers1,5952
Water1,09961
1
A: Apo-(GRAND CoilSerL12(DLE)L16C)3
hetero molecules

A: Apo-(GRAND CoilSerL12(DLE)L16C)3
hetero molecules

A: Apo-(GRAND CoilSerL12(DLE)L16C)3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1309
Polymers12,3443
Non-polymers4,7866
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area4460 Å2
ΔGint-115 kcal/mol
Surface area7100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.213, 38.213, 140.655
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-204-

HOH

21A-231-

HOH

31A-255-

HOH

41A-261-

HOH

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Components

#1: Protein/peptide Apo-(GRAND CoilSerL12(DLE)L16C)3


Mass: 4114.800 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES, pH 6.5, 25% PEG2000 MME / PH range: 6.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 27, 2014
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 8486 / % possible obs: 99.3 % / Redundancy: 10.4 % / Biso Wilson estimate: 21.74 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.021 / Rrim(I) all: 0.066 / Χ2: 1.083 / Net I/σ(I): 10.5 / Num. measured all: 88359
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.38-1.410.40.5314160.9280.1730.5580.411100
1.4-1.4310.50.4284150.9420.1390.450.433100
1.43-1.4610.50.3864060.9470.1250.4060.46100
1.46-1.4910.60.2594260.9880.0840.2730.469100
1.49-1.5210.50.2014220.9940.0650.2110.531100
1.52-1.5510.60.1994050.9910.0640.2090.557100
1.55-1.5910.60.1694310.9910.0550.1780.58100
1.59-1.6410.60.1454110.9950.0470.1530.601100
1.64-1.6810.50.1264260.9940.0410.1330.662100
1.68-1.7410.50.1124390.9940.0360.1180.682100
1.74-1.810.70.0954050.9970.030.10.782100
1.8-1.8710.60.0854240.9980.0270.0890.866100
1.87-1.9610.50.0734190.9980.0230.0760.911100
1.96-2.0610.70.0674310.9980.0210.0711.056100
2.06-2.1910.50.0714270.9980.0230.0751.523100
2.19-2.3610.60.0794350.9970.0250.0832.182100
2.36-2.610.50.0754310.9970.0240.0792.391100
2.6-2.9710.50.0624410.9980.020.0652.186100
2.97-3.75100.0484440.9980.0160.0512.00399.1
3.75-508.50.0544320.9950.020.0582.44489.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LJM

3ljm


Resolution: 1.4→9.28 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.967 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.069 / SU Rfree Blow DPI: 0.062 / SU Rfree Cruickshank DPI: 0.057
RfactorNum. reflection% reflectionSelection details
Rfree0.184 380 4.7 %RANDOM
Rwork0.177 ---
obs0.177 8093 99.5 %-
Displacement parametersBiso max: 91.06 Å2 / Biso mean: 30.96 Å2 / Biso min: 9.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.6951 Å20 Å20 Å2
2---0.6951 Å20 Å2
3---1.3901 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: final / Resolution: 1.4→9.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms283 0 8 61 352
Biso mean--30.51 34.58 -
Num. residues----36
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d176SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes11HARMONIC2
X-RAY DIFFRACTIONt_gen_planes101HARMONIC5
X-RAY DIFFRACTIONt_it688HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion43SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact813SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d702HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1304HARMONIC21.26
X-RAY DIFFRACTIONt_omega_torsion2.45
X-RAY DIFFRACTIONt_other_torsion16.51
LS refinement shellResolution: 1.4→1.56 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.173 105 4.64 %
Rwork0.157 2159 -
all0.158 2264 -
obs--100 %
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)
1-0.0598-0.1708-0.35360.7709-2.976813.0014-0.17070.0263-0.0084-0.07720.0676-0.01610.386-0.55220.1030.001-0.06120.00840.04960.0222-0.05134.90593.111119.3821
21.9065-0.44420.14143.5104-1.56026.11980.01160.03150.1477-0.0248-0.0372-0.1415-0.16320.02110.0255-0.03170.0211-0.0056-0.01030.0183-0.00196.016-1.735944.1483
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 25}A1 - 25
2X-RAY DIFFRACTION2{A|26 - 36}A26 - 36

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