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- PDB-5ier: Structure of a computationally designed 17-OHP binder -

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Basic information

Entry
Database: PDB / ID: 5ier
TitleStructure of a computationally designed 17-OHP binder
ComponentsOHP9
KeywordsDE NOVO PROTEIN / Rossetta / ligand binder / computational / Structural Genomics
Function / homologyNuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / (9beta)-17-hydroxypregn-4-ene-3,20-dione
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.005 Å
AuthorsStoddard, B.L. / Doyle, L.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115545 United States
CitationJournal: Protein Sci. / Year: 2017
Title: Sampling and energy evaluation challenges in ligand binding protein design.
Authors: Dou, J. / Doyle, L. / Jr Greisen, P. / Schena, A. / Park, H. / Johnsson, K. / Stoddard, B.L. / Baker, D.
History
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OHP9
B: OHP9
C: OHP9
D: OHP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,35017
Polymers57,4564
Non-polymers1,89413
Water5,224290
1
A: OHP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9336
Polymers14,3641
Non-polymers5695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: OHP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7913
Polymers14,3641
Non-polymers4272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: OHP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7913
Polymers14,3641
Non-polymers4272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: OHP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8375
Polymers14,3641
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.832, 78.832, 184.478
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
OHP9


Mass: 14364.079 Da / Num. of mol.: 4 / Fragment: computational design
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-3QZ / (9beta)-17-hydroxypregn-4-ene-3,20-dione / 17α-Hydroxyprogesterone


Mass: 330.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30O3 / Comment: hormone*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5, 1% PEG400, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2015
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 45418 / % possible obs: 100 % / Redundancy: 10.2 % / Biso Wilson estimate: 29.96 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.022 / Rrim(I) all: 0.071 / Χ2: 1.098 / Net I/av σ(I): 33.66 / Net I/σ(I): 14.8 / Num. measured all: 464654
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.077.40.369199.8
2.07-2.15100.2811100
2.15-2.2510.30.2131100
2.25-2.3710.50.1691100
2.37-2.5210.60.1331100
2.52-2.7110.80.1071100
2.71-2.9910.90.0751100
2.99-3.4210.90.0591100
3.42-4.3110.70.0591100
4.31-5010.10.044199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.01 Å36.25 Å
Translation2.01 Å36.25 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.6phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A15

2a15


Resolution: 2.005→36.245 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.53
RfactorNum. reflection% reflection
Rfree0.2098 2015 4.44 %
Rwork0.1777 --
obs0.1791 45359 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.3 Å2 / Biso mean: 39.1806 Å2 / Biso min: 15.15 Å2
Refinement stepCycle: final / Resolution: 2.005→36.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3875 0 245 290 4410
Biso mean--50.02 41.47 -
Num. residues----519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034092
X-RAY DIFFRACTIONf_angle_d0.6885607
X-RAY DIFFRACTIONf_chiral_restr0.029650
X-RAY DIFFRACTIONf_plane_restr0.002696
X-RAY DIFFRACTIONf_dihedral_angle_d11.6811386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0055-2.05560.24551400.21982990313099
2.0556-2.11120.24781430.208730783221100
2.1112-2.17330.26561420.198730593201100
2.1733-2.24350.22061410.18830573198100
2.2435-2.32360.23451450.186430423187100
2.3236-2.41670.22541390.195330483187100
2.4167-2.52660.22981420.190430873229100
2.5266-2.65980.22411420.191830543196100
2.6598-2.82640.24431460.207231143260100
2.8264-3.04450.23881400.18630853225100
3.0445-3.35070.23371450.195331133258100
3.3507-3.83510.18911470.161431163263100
3.8351-4.830.16461480.143931733321100
4.83-36.25130.19331550.170233283483100

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