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- PDB-3kdm: Crystal Structure of Human Anti-steroid Fab 5F2 in Complex with T... -

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Basic information

Entry
Database: PDB / ID: 3kdm
TitleCrystal Structure of Human Anti-steroid Fab 5F2 in Complex with Testosterone
Components
  • Immunoglobulin heavy chain
  • Immunoglobulin light chain
KeywordsIMMUNE SYSTEM / Antibody / Immunoglobulin Fab fragment / Anti-steroid
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / TESTOSTERONE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNiemi, M.H. / Rouvinen, J.
CitationJournal: J.Mol.Recognit. / Year: 2010
Title: The testosterone binding mechanism of an antibody derived from a naive human scFv library
Authors: Niemi, M.H. / Takkinen, K. / Amundsen, L.K. / Soderlund, H. / Rouvinen, J. / Hoyhtya, M.
History
DepositionOct 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 7, 2011Group: Database references
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Immunoglobulin light chain
H: Immunoglobulin heavy chain
A: Immunoglobulin light chain
B: Immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7776
Polymers94,2004
Non-polymers5772
Water16,556919
1
L: Immunoglobulin light chain
H: Immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3893
Polymers47,1002
Non-polymers2881
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-29 kcal/mol
Surface area18840 Å2
MethodPISA
2
A: Immunoglobulin light chain
B: Immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3893
Polymers47,1002
Non-polymers2881
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-29 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.750, 67.080, 67.060
Angle α, β, γ (deg.)81.320, 69.300, 69.270
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Immunoglobulin light chain /


Mass: 23373.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): RV308
#2: Antibody Immunoglobulin heavy chain /


Mass: 23726.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): RV308
#3: Chemical ChemComp-TES / TESTOSTERONE / Testosterone


Mass: 288.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H28O2 / Comment: hormone*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 919 / 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: 55.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 12% PEG 3350, 0.1M sodium citrate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0091 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0091 Å / Relative weight: 1
Reflection twinOperator: -h,-l,-k / Fraction: 0.501
ReflectionResolution: 1.5→50 Å / Num. all: 163180 / Num. obs: 151891 / % possible obs: 93.1 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.033
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 2 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.47 / % possible all: 91

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MHP

1mhp


Resolution: 1.5→48.25 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.832 / σ(F): 1.99
RfactorNum. reflection% reflectionSelection details
Rfree0.208 8100 5.33 %random
Rwork0.18 ---
obs0.181 151891 93.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.896 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso max: 59.06 Å2 / Biso mean: 20.116 Å2 / Biso min: 10.81 Å2
Baniso -1Baniso -2Baniso -3
1--4.805 Å20.84 Å21.11 Å2
2--2.126 Å2-5.291 Å2
3---2.679 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6564 0 42 919 7525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136781
X-RAY DIFFRACTIONf_angle_d1.6589233
X-RAY DIFFRACTIONf_chiral_restr0.0981040
X-RAY DIFFRACTIONf_plane_restr0.0071176
X-RAY DIFFRACTIONf_dihedral_angle_d18.9332379
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.5260.283680.28269957363
1.526-1.5540.2883730.27670897462
1.554-1.5840.2623750.26371227497
1.584-1.6160.283800.25272137593
1.616-1.6510.2743740.25571147488
1.651-1.690.2753810.24872287609
1.69-1.7320.253770.24971777554
1.732-1.7790.2543800.24272157595
1.779-1.8310.2583780.2471767554
1.831-1.890.2343800.22472257605
1.89-1.9580.2453820.22172527634
1.958-2.0360.2353800.21472227602
2.036-2.1290.2283800.20172147594
2.129-2.2410.2243860.19673467732
2.241-2.3820.2123850.19373047689
2.382-2.5660.2173830.19172927675
2.566-2.8240.2093840.17472967680
2.824-3.2320.2043810.15172397620
3.232-4.0720.1523830.11872737656
4.072-48.2760.1473850.11773047689

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