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- PDB-5vnv: Crystal structure of Nb.b201 -

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Basic information

Entry
Database: PDB / ID: 5vnv
TitleCrystal structure of Nb.b201
ComponentsNb.b201
KeywordsDE NOVO PROTEIN / nanobody / synthetic protein / llama / camelid
Function / homologyFORMIC ACID / :
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKruse, A.C. / McMahon, C.
Funding support United States, 2items
OrganizationGrant numberCountry
Smith Family Foundation United States
National Institutes of Health/Office of the Director1DP5OD021345 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Yeast surface display platform for rapid discovery of conformationally selective nanobodies.
Authors: McMahon, C. / Baier, A.S. / Pascolutti, R. / Wegrecki, M. / Zheng, S. / Ong, J.X. / Erlandson, S.C. / Hilger, D. / Rasmussen, S.G.F. / Ring, A.M. / Manglik, A. / Kruse, A.C.
History
DepositionMay 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Oct 4, 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_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.ptnr1_symmetry / _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_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nb.b201
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2679
Polymers13,3501
Non-polymers9178
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.751, 106.751, 52.232
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-201-

1PE

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Components

#1: Antibody Nb.b201


Mass: 13349.759 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Potassium formate, BIS-TRIS propane pH 9, PEG MME 2000, Sodium chloride, HEPES pH 7.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 28, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.4→46.9 Å / Num. obs: 29224 / % possible obs: 97.3 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rsym value: 0.077 / Net I/σ(I): 11.85
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4153 / CC1/2: 0.56 / Rsym value: 0.888 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575-0000)refinement
XDSNov 1, 2016data reduction
XDSNov 1, 2016data scaling
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IMM

5imm


Resolution: 1.4→46.9 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.62
RfactorNum. reflection% reflection
Rfree0.2136 2777 5.03 %
Rwork0.183 --
obs0.1844 29221 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms923 0 39 134 1096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008999
X-RAY DIFFRACTIONf_angle_d0.9941348
X-RAY DIFFRACTIONf_dihedral_angle_d19.699361
X-RAY DIFFRACTIONf_chiral_restr0.089143
X-RAY DIFFRACTIONf_plane_restr0.005169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3983-1.42240.30691050.30371942X-RAY DIFFRACTION72
1.4224-1.44830.31621250.30582335X-RAY DIFFRACTION86
1.4483-1.47620.331370.27912557X-RAY DIFFRACTION96
1.4762-1.50630.25431420.26582696X-RAY DIFFRACTION98
1.5063-1.5390.26621400.25322643X-RAY DIFFRACTION98
1.539-1.57480.31151380.25932657X-RAY DIFFRACTION99
1.5748-1.61420.25881410.24742656X-RAY DIFFRACTION99
1.6142-1.65790.24221450.23212696X-RAY DIFFRACTION98
1.6579-1.70670.21891410.22042678X-RAY DIFFRACTION99
1.7067-1.76180.21531420.18762659X-RAY DIFFRACTION99
1.7618-1.82470.22471410.19212703X-RAY DIFFRACTION99
1.8247-1.89780.24451480.18442682X-RAY DIFFRACTION99
1.8978-1.98420.21941390.16712700X-RAY DIFFRACTION99
1.9842-2.08880.19691410.16132706X-RAY DIFFRACTION99
2.0888-2.21960.17321410.16032706X-RAY DIFFRACTION100
2.2196-2.3910.1841440.17462673X-RAY DIFFRACTION100
2.391-2.63160.21451410.18092700X-RAY DIFFRACTION100
2.6316-3.01230.21081450.1782707X-RAY DIFFRACTION100
3.0123-3.7950.18421380.1612719X-RAY DIFFRACTION100
3.795-46.94340.21321470.16782710X-RAY DIFFRACTION100
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)
10.12480.00770.10760.03730.04350.1245-0.0870.1953-0.3388-0.5219-0.0115-0.25440.49760.43450.00710.31040.04220.06180.2557-0.04160.232816.3492-14.960110.3239
21.64270.26390.15970.53990.1660.1621-0.1098-0.21940.017-0.1531-0.0675-0.00750.1040.088-0.09910.27510.0009-0.00440.11010.00390.19892.42-25.17623.6146
30.10660.0483-0.05860.23470.11560.0502-0.19390.14120.3071-0.16360.3090.11850.32890.07570.00130.21710.0418-0.00010.2004-0.00380.164612.1907-15.775418.9974
40.20210.2057-0.08590.4551-0.68671.00760.03770.0414-0.0479-0.18450.0166-0.11350.19910.16540.00190.16570.0104-0.00350.1758-0.020.180111.1176-6.666811.9699
50.9955-0.4290.01061.0316-1.38661.38570.06180.02750.0153-0.34050.0480.19850.2462-0.11290.11360.1942-0.014-0.0530.1518-0.0070.16592.0071-8.073914.3029
60.03080.0123-0.17920.6126-0.27160.9870.06920.023-0.0596-0.0073-0.00250.03120.1490.090200.14440.0132-0.01620.1488-0.01180.15976.952-9.807420.8731
70.4143-0.42710.05780.7425-0.02880.3824-0.02280.0571-0.0242-0.27740.01990.15950.3505-0.0682-0.00070.2721-0.0265-0.05920.1587-0.02710.18842.0637-16.890115.4317
80.04720.10750.11680.24090.43650.586-0.03740.1450.0212-0.6740.14290.05620.05060.12180.00010.27830.01880.0050.2092-0.01590.174310.5793-4.71884.3978
90.5068-0.20420.28940.1228-0.05730.1309-0.1809-0.2138-0.423-0.5666-0.09490.19950.3814-0.0417-0.02540.3547-0.01790.01130.1431-0.01140.2730.1722-27.426818.8231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 7 )
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 17 )
3X-RAY DIFFRACTION3chain 'A' and (resid 18 through 24 )
4X-RAY DIFFRACTION4chain 'A' and (resid 25 through 39 )
5X-RAY DIFFRACTION5chain 'A' and (resid 40 through 59 )
6X-RAY DIFFRACTION6chain 'A' and (resid 60 through 82 )
7X-RAY DIFFRACTION7chain 'A' and (resid 83 through 98 )
8X-RAY DIFFRACTION8chain 'A' and (resid 99 through 111 )
9X-RAY DIFFRACTION9chain 'A' and (resid 112 through 120 )

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