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- PDB-6xxp: Crystal structure of NB37, a nanobody targeting prostate specific... -

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Basic information

Entry
Database: PDB / ID: 6xxp
TitleCrystal structure of NB37, a nanobody targeting prostate specific membrane antigen
ComponentsNB_37
KeywordsANTITUMOR PROTEIN / Nanobody / prostate-specific membrane antigen / antibody drug conjugate / cancer imaging / anti-cancer drugs.
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsShahar, A. / Rosenfeld, L. / Papo, N.
Funding support Israel, 1items
OrganizationGrant numberCountry
European Research Council (ERC)336041 Israel
CitationJournal: J.Med.Chem. / Year: 2020
Title: Nanobodies Targeting Prostate-Specific Membrane Antigen for the Imaging and Therapy of Prostate Cancer.
Authors: Rosenfeld, L. / Sananes, A. / Zur, Y. / Cohen, S. / Dhara, K. / Gelkop, S. / Ben Zeev, E. / Shahar, A. / Lobel, L. / Akabayov, B. / Arbely, E. / Papo, N.
History
DepositionJan 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NB_37


Theoretical massNumber of molelcules
Total (without water)15,7151
Polymers15,7151
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.949, 69.087, 75.869
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-255-

HOH

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Components

#1: Protein NB_37


Mass: 15715.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M tri-Na Citrate pH 3.5, 25% peg 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.5→27.41 Å / Num. obs: 23658 / % possible obs: 98.84 % / Redundancy: 4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0529 / Net I/σ(I): 14.42
Reflection shellResolution: 1.5→1.59 Å / Num. unique obs: 3756 / CC1/2: 0.796 / Rrim(I) all: 0.536

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M7Q

5m7q


Resolution: 1.5→27.41 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.19
RfactorNum. reflection% reflection
Rfree0.1956 1149 4.86 %
Rwork0.1723 --
obs0.1734 23649 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→27.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 0 124 1087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051068
X-RAY DIFFRACTIONf_angle_d0.8081464
X-RAY DIFFRACTIONf_dihedral_angle_d8.117582
X-RAY DIFFRACTIONf_chiral_restr0.079154
X-RAY DIFFRACTIONf_plane_restr0.004196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.56790.26651300.23592761X-RAY DIFFRACTION99
1.5679-1.65050.26631660.21622789X-RAY DIFFRACTION100
1.6505-1.75390.22441420.19832798X-RAY DIFFRACTION100
1.7539-1.88930.20211340.18072833X-RAY DIFFRACTION100
1.8893-2.07940.19981300.17022813X-RAY DIFFRACTION99
2.0794-2.38020.23031550.17542796X-RAY DIFFRACTION99
2.3802-2.99820.19941350.17822783X-RAY DIFFRACTION97
2.9982-3.180.15751570.14942927X-RAY DIFFRACTION98
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)
12.3595-0.7262-0.55086.79520.29950.13120.2953-0.03650.4785-0.01910.3745-0.7505-0.48760.7783-0.61020.1489-0.03850.01340.2248-0.05860.2389-6.0242-17.68595.9398
24.17284.24954.52597.00342.51016.7224-0.32990.3553-0.1341-0.47270.20760.01330.38050.54590.06140.12660.03040.03870.15620.00070.1235-7.6779-28.2743-14.6958
31.0819-0.6794-1.47310.42581.00016.287-0.0155-0.06720.07410.10390.0287-0.05950.29180.01020.01330.161-0.0218-0.00780.1192-0.01720.1382-12.3287-22.54068.5332
46.18160.4715-2.32455.0563-2.75795.23540.1742-0.06860.19550.0240.07180.084-0.28320.1226-0.18280.0913-0.0154-0.0030.0617-0.03360.0982-16.9472-19.7153-0.8507
53.03262.1856-3.58834.102-2.77264.2580.21970.29940.34980.06710.09970.1427-0.4811-0.2892-0.11760.14470.01920.03070.13030.02210.1416-19.6606-17.4292-6.3297
62.67090.74231.7534.26680.60241.4440.15890.3517-0.3226-0.188-0.18380.17880.5528-0.3898-0.12140.213-0.0133-0.03260.2806-0.04180.1727-23.8434-28.0187-2.3947
74.29371.64712.74214.08851.93416.55220.0462-0.02940.0059-0.0136-0.0737-0.08220.035-0.07670.03620.12340.01270.00590.05990.0030.0964-13.1331-29.42971.6369
81.8961-1.1770.38129.3149-7.31416.66330.13630.0164-0.0049-0.4190.12060.36630.412-0.1192-0.29520.1845-0.0237-0.00840.13320.01350.1078-15.5104-27.2918-15.8254
92.27380.1608-1.31.35550.79677.1970.063-0.14070.1681-0.0488-0.00110.0218-0.3311-0.1425-0.07210.14840.0044-0.00420.1026-0.00430.1423-18.4296-15.93053.3521
103.2173-0.7855-0.98620.83890.15231.9921-0.10880.4122-0.2552-0.44070.14770.05480.28820.53210.02060.28880.00360.01550.16060.00450.1287-9.1087-23.3138-17.9045
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 32 )
4X-RAY DIFFRACTION4chain 'A' and (resid 33 through 39 )
5X-RAY DIFFRACTION5chain 'A' and (resid 40 through 52 )
6X-RAY DIFFRACTION6chain 'A' and (resid 53 through 67 )
7X-RAY DIFFRACTION7chain 'A' and (resid 68 through 83 )
8X-RAY DIFFRACTION8chain 'A' and (resid 84 through 91 )
9X-RAY DIFFRACTION9chain 'A' and (resid 92 through 117 )
10X-RAY DIFFRACTION10chain 'A' and (resid 118 through 127 )

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