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- PDB-1ay1: ANTI TAQ FAB TP7 -

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Basic information

Entry
Database: PDB / ID: 1ay1
TitleANTI TAQ FAB TP7
Components(TP7 FAB) x 2
KeywordsIMMUNOGLOBULIN / ANTIBODY / FAB / ENZYME INHIBITOR / PCR / HOT START
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMurali, R. / Helmer-Citterich, M. / Sharkey, D.J. / Scalice, E.R. / Daiss, J.L. / Sullivan, M.A. / Murthy, H.M.K.
CitationJournal: Protein Eng. / Year: 1998
Title: Structural studies on an inhibitory antibody against Thermus aquaticus DNA polymerase suggest mode of inhibition.
Authors: Murali, R. / Helmer-Citterich, M. / Sharkey, D.J. / Scalice, E.R. / Daiss, J.L. / Sullivan, M.A. / Krishna Murthy, H.M.
History
DepositionNov 13, 1997Processing site: BNL
Revision 1.0May 13, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 2, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
L: TP7 FAB
H: TP7 FAB


Theoretical massNumber of molelcules
Total (without water)46,6732
Polymers46,6732
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-23 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.500, 72.700, 82.200
Angle α, β, γ (deg.)90.00, 98.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody TP7 FAB


Mass: 23082.521 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q91W12
#2: Antibody TP7 FAB


Mass: 23590.266 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 1513182
Has protein modificationY
Sequence detailsTHE FAB LIGHT CHAIN HAS BEEN ASSIGNED CHAIN INDICATOR *L*. THE FAB HEAVY CHAIN HAS BEEN ASSIGNED ...THE FAB LIGHT CHAIN HAS BEEN ASSIGNED CHAIN INDICATOR *L*. THE FAB HEAVY CHAIN HAS BEEN ASSIGNED CHAIN INDICATOR *H*. FRAGMENT IS NUMBERED ACCORDING TO THE NUMBER CONVENTION OF E. KABAT (E.A.KABAT,T.T.WU,M.REID-MILLER,H.M.PERRY, K.S.GOTTESMAN (1987) SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 4TH ED., NATIONAL INSTITUTES OF HEALTH, BETHESDA, MD) INSERTIONS IN HYPERVARIABLE REGIONS WITH RESPECT TO THE CANONICAL SEQUENCE HAVE BEEN DESIGNATED BY SUFFIXES OF A,B, ETC.. THERE IS ONE DELETION AT RESIDUE 28 IN THE L CHAIN COMPARED TO THE CANONICAL SEQUENCE. THUS NO RESIDUE WITH NUMBER 28 EXISTS IN THE LIGHT CHAIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 9
Details: PROTEIN WAS CRYSTALLIZED FROM 16% PEG3350, 0.4% BETA OCTYL GLUCOSIDE, 100MM TRIS, PH 9.0
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mg/mlprotein1drop
20.2 %beta-octylglucoside1drop
360 mMTris-HCl1drop
48 %PEG33501drop
516 %PEG33501reservoir
6100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 50786 / % possible obs: 83 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.056 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.112 / Mean I/σ(I) obs: 4.8 / Rsym value: 0.068 / % possible all: 68.2
Reflection shell
*PLUS
% possible obs: 68.2 %

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
AMoREphasing
X-PLOR3.1refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HIL

1hil


Resolution: 2.2→7 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: SIDE CHAINS OF RESIDUES 130 - 134 IN THE HEAVY CHAIN ARE DISORDERED AND ARE MODELED TO BE IN THEIR MOST PROBABLE CONFORMATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1669 8.6 %RANDOM
Rwork0.196 ---
obs0.196 19212 82.5 %-
Displacement parametersBiso mean: 21.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å / Luzzati d res low obs: 7 Å
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 0 0 3282
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d18.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.71
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.52
X-RAY DIFFRACTIONx_mcangle_it1.52
X-RAY DIFFRACTIONx_scbond_it22.5
X-RAY DIFFRACTIONx_scangle_it22.5
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.319 105 11.5 %
Rwork0.239 908 -
obs--68.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1F / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg18.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.71
LS refinement shell
*PLUS
Rfactor obs: 0.239

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