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- PDB-6ksn: Structure of a Zn-bound camelid single domain antibody -

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Basic information

Entry
Database: PDB / ID: 6ksn
TitleStructure of a Zn-bound camelid single domain antibody
ComponentsICab3
KeywordsMETAL BINDING PROTEIN / Indian Camelid Single domain Antibody / VHH
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKumar, S. / Athreya, A. / Penmatsa, A.
Funding support India, 2items
OrganizationGrant numberCountry
Wellcome TrustIA/1/15/2/502063 India
Department of Biotechnology (India)BT/09/IYBA/2015/13 India
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Isolation and structural characterization of a Zn2+-bound single-domain antibody against NorC, a putative multidrug efflux transporter in bacteria.
Authors: Kumar, S. / Mahendran, I. / Athreya, A. / Ranjan, R. / Penmatsa, A.
History
DepositionAug 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
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.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.value / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ICab3
B: ICab3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,59523
Polymers29,3242
Non-polymers1,27121
Water2,180121
1
A: ICab3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,22410
Polymers14,6621
Non-polymers5629
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6560 Å2
MethodPISA
2
B: ICab3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,37113
Polymers14,6621
Non-polymers70912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area6910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.880, 106.880, 70.580
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTRPTRP(chain 'A' and (resid 4 through 91 or (resid 92...AA4 - 1254 - 125
12GLYGLYSERSER(chain 'A' and (resid 4 through 91 or (resid 92...AA128 - 134128 - 134
23SERSERTRPTRP(chain 'B' and (resid 4 or (resid 5 and (name...BB4 - 1254 - 125
24GLYGLYSERSER(chain 'B' and (resid 4 or (resid 5 and (name...BB128 - 134128 - 134

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Components

#1: Protein ICab3


Mass: 14662.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Gene: VHH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.03 Å3/Da / Density % sol: 69.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.25 / Details: 0.1M Tris, pH8.25, 3.5M Na Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 25502 / % possible obs: 99.6 % / Observed criterion σ(I): 1.9 / Redundancy: 8.9 % / Biso Wilson estimate: 31.12 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0123 / Rpim(I) all: 0.045 / Rrim(I) all: 0.138 / Net I/σ(I): 11.1
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 8 % / Rmerge(I) obs: 1.146 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2171 / CC1/2: 0.624 / Rpim(I) all: 0.422 / Rrim(I) all: 1.223 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JBE

3jbe


Resolution: 2.15→46.28 Å / SU ML: 0.2226 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4642
RfactorNum. reflection% reflection
Rfree0.2324 1295 5.08 %
Rwork0.1932 --
obs0.1952 25479 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 59.59 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 75 121 2195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632109
X-RAY DIFFRACTIONf_angle_d0.91422818
X-RAY DIFFRACTIONf_chiral_restr0.0535291
X-RAY DIFFRACTIONf_plane_restr0.0053361
X-RAY DIFFRACTIONf_dihedral_angle_d5.83521394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.240.27231290.26342641X-RAY DIFFRACTION98.86
2.24-2.340.2851550.24482627X-RAY DIFFRACTION98.86
2.34-2.460.28781340.25332652X-RAY DIFFRACTION98.83
2.46-2.620.30261300.23842696X-RAY DIFFRACTION99.16
2.62-2.820.26521610.22362626X-RAY DIFFRACTION99.68
2.82-3.10.2731320.22452709X-RAY DIFFRACTION99.61
3.1-3.550.24051550.18422690X-RAY DIFFRACTION99.93
3.55-4.470.1921590.15652714X-RAY DIFFRACTION100
4.47-46.280.19531400.16792829X-RAY DIFFRACTION99.6
Refinement TLS params.Method: refined / Origin x: 8.78987484667 Å / Origin y: -42.5000931767 Å / Origin z: 12.0704106222 Å
111213212223313233
T0.228548882658 Å2-0.0586053134316 Å20.0374880982839 Å2-0.754094575263 Å2-0.0341910240884 Å2--0.440625120325 Å2
L4.60094700689 °20.229964070832 °21.94934274451 °2-0.89671584183 °2-0.032479798848 °2--0.885528012713 °2
S-0.0376380318862 Å °0.311262166194 Å °0.298202314603 Å °-0.109376302786 Å °-0.0144334959777 Å °0.093552700847 Å °-0.490778683779 Å °-0.11821787594 Å °0.0653272631851 Å °
Refinement TLS groupSelection details: all

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