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- PDB-32c2: STRUCTURE OF AN ACTIVITY SUPPRESSING FAB FRAGMENT TO CYTOCHROME P... -

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Basic information

Entry
Database: PDB / ID: 32c2
TitleSTRUCTURE OF AN ACTIVITY SUPPRESSING FAB FRAGMENT TO CYTOCHROME P450 AROMATASE
Components(IGG1 ANTIBODY 32C2) x 2
KeywordsIMMUNE SYSTEM / FAB / ANTIBODY / AROMATASE / P450
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSawicki, M.W. / Ng, P.C. / Burkhart, B. / Pletnev, V. / Higashiyama, T. / Osawa, Y. / Ghosh, D.
CitationJournal: Mol.Immunol. / Year: 1999
Title: Structure of an activity suppressing Fab fragment to cytochrome P450 aromatase: insights into the antibody-antigen interactions.
Authors: Sawicki, M.W. / Ng, P.C. / Burkhart, B.M. / Pletnev, V.Z. / Higashiyama, T. / Osawa, Y. / Ghosh, D.
History
DepositionApr 21, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: 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 1.4Oct 16, 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: IGG1 ANTIBODY 32C2
B: IGG1 ANTIBODY 32C2


Theoretical massNumber of molelcules
Total (without water)47,2952
Polymers47,2952
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-24 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.890, 73.510, 36.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody IGG1 ANTIBODY 32C2


Mass: 23827.373 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN, VARIABLE REGION / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody IGG1 ANTIBODY 32C2


Mass: 23468.115 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, VARIABLE REGION / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growpH: 4.4
Details: 0.2M SODIUM ACETATE, PH 4.4 @ 12 MG/ML. PRECIPITANT WAS 25% PEG 3350, pH 4.40
Crystal
*PLUS
Density % sol: 51 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 5 / PH range high: 4.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 Msodium acetate1drop
210 mMsodium azide1drop
312 mg/mlFab1drop
425 %PEG33501reservoir
50.2 Msodium acetate1reservoir
610 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→99 Å / Num. obs: 9161 / % possible obs: 91.1 % / Observed criterion σ(I): 2 / Rsym value: 0.091
Reflection shellResolution: 3→3.19 Å / % possible all: 71.9
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 99 Å / % possible obs: 91.1 % / Observed criterion σ(I): 2 / Num. measured all: 42185 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.19 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNS0.4refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FLR

1flr


Resolution: 3→99 Å / Rfactor Rfree error: 0.011 / Data cutoff high rms absF: 196784 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.317 808 10.2 %RANDOM
Rwork0.213 ---
obs-7950 88.3 %-
Displacement parametersBiso mean: 45 Å2
Baniso -1Baniso -2Baniso -3
1-5 Å20 Å20 Å2
2---8.99 Å20 Å2
3---3.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 3→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3326 0 0 0 3326
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d1.052
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.431.5
X-RAY DIFFRACTIONc_mcangle_it6.92
X-RAY DIFFRACTIONc_scbond_it5.52
X-RAY DIFFRACTIONc_scangle_it7.662.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 94 8.9 %
Rwork0.264 966 -
obs--71.9 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 99 Å / Rfactor obs: 0.2124
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.18
X-RAY DIFFRACTIONc_mcbond_it4.43
X-RAY DIFFRACTIONc_scbond_it5.5
X-RAY DIFFRACTIONc_mcangle_it6.9
X-RAY DIFFRACTIONc_scangle_it7.66
LS refinement shell
*PLUS
Rfactor Rfree: 0.344 / Rfactor Rwork: 0.264

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