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- PDB-5muq: Crystal structure of DC8E8 Fab at pH 7.0 containing a Zn atom -

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Basic information

Entry
Database: PDB / ID: 5muq
TitleCrystal structure of DC8E8 Fab at pH 7.0 containing a Zn atom
Components
  • antibody Fab heavy chain
  • antibody kappa light chain
KeywordsIMMUNE SYSTEM / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / IMIDAZOLE
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.62 Å
AuthorsSkrabana, R. / Novak, M. / Cehlar, O. / Kontsekova, E.
CitationJournal: To be published
Title: Crystal structure of DC8E8 Fab at pH 7.0 containing a Zn atom
Authors: Skrabana, R. / Novak, M. / Cehlar, O. / Kontsekova, E.
History
DepositionJan 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jan 17, 2024Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
H: antibody Fab heavy chain
L: antibody kappa light chain
A: antibody Fab heavy chain
B: antibody kappa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1928
Polymers95,9234
Non-polymers2694
Water48627
1
H: antibody Fab heavy chain
L: antibody kappa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0964
Polymers47,9612
Non-polymers1342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-48 kcal/mol
Surface area20340 Å2
MethodPISA
2
A: antibody Fab heavy chain
B: antibody kappa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0964
Polymers47,9612
Non-polymers1342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-49 kcal/mol
Surface area20360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.510, 113.510, 69.390
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Antibody antibody Fab heavy chain


Mass: 23685.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody antibody kappa light chain


Mass: 24275.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 16% PEG 3350, 0.2 M imidazol, 0.02 M ZnSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8166 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8166 Å / Relative weight: 1
ReflectionResolution: 2.616→98.3 Å / Num. obs: 29733 / % possible obs: 98.5 % / Redundancy: 5.8 % / Rrim(I) all: 0.05 / Net I/σ(I): 28.47
Reflection shellResolution: 2.616→2.67 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.16 / Num. unique all: 1802 / CC1/2: 0.794 / Rrim(I) all: 0.804 / % possible all: 80.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
XDSdata reduction
PHASERphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4OZ4

4oz4
PDB Unreleased entry


Resolution: 2.62→98.3 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.9 / SU B: 15.645 / SU ML: 0.319 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.271 / ESU R Free: 0.365
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2794 1503 5.1 %RANDOM
Rwork0.2122 ---
obs0.2156 28230 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 176.4 Å2 / Biso mean: 73.988 Å2 / Biso min: 34.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å20.83 Å20 Å2
2--1.66 Å20 Å2
3----5.38 Å2
Refinement stepCycle: final / Resolution: 2.62→98.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6683 0 12 27 6722
Biso mean--112.21 54.22 -
Num. residues----878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.026865
X-RAY DIFFRACTIONr_bond_other_d0.0020.026074
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9489337
X-RAY DIFFRACTIONr_angle_other_deg1.033314187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0815874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41124.264258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.321151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9351524
X-RAY DIFFRACTIONr_chiral_restr0.0910.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217590
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021382
LS refinement shellResolution: 2.616→2.684 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 80 -
Rwork0.375 1714 -
all-1794 -
obs--80.05 %

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