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- PDB-1fl6: THE HAPTEN COMPLEXED GERMLINE PRECURSOR TO SULFIDE OXIDASE CATALY... -

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Basic information

Entry
Database: PDB / ID: 1fl6
TitleTHE HAPTEN COMPLEXED GERMLINE PRECURSOR TO SULFIDE OXIDASE CATALYTIC ANTIBODY 28B4
Components(ANTIBODY GERMLINE PRECURSOR TO 28B4) x 2
KeywordsIMMUNE SYSTEM / catalytic antibody / germline antibody / sulfide oxidase
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-AAH
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsYin, J. / Mundorff, E.C. / Yang, P.L. / Wendt, K.U. / Hanway, D. / Stevens, R.C. / Schultz, P.G.
CitationJournal: Biochemistry / Year: 2001
Title: A comparative analysis of the immunological evolution of antibody 28B4.
Authors: Yin, J. / Mundorff, E.C. / Yang, P.L. / Wendt, K.U. / Hanway, D. / Stevens, R.C. / Schultz, P.G.
History
DepositionAug 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: ANTIBODY GERMLINE PRECURSOR TO 28B4
H: ANTIBODY GERMLINE PRECURSOR TO 28B4
A: ANTIBODY GERMLINE PRECURSOR TO 28B4
B: ANTIBODY GERMLINE PRECURSOR TO 28B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0446
Polymers94,3514
Non-polymers6932
Water00
1
L: ANTIBODY GERMLINE PRECURSOR TO 28B4
H: ANTIBODY GERMLINE PRECURSOR TO 28B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5223
Polymers47,1762
Non-polymers3461
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-17 kcal/mol
Surface area19410 Å2
MethodPISA
2
A: ANTIBODY GERMLINE PRECURSOR TO 28B4
B: ANTIBODY GERMLINE PRECURSOR TO 28B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5223
Polymers47,1762
Non-polymers3461
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-20 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.460, 127.610, 65.590
Angle α, β, γ (deg.)90.00, 104.62, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe bioliogical assembly is constructed from chain L and H. Chains A and B contruct another biological unit related through non-crystallographic symmetry

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Components

#1: Antibody ANTIBODY GERMLINE PRECURSOR TO 28B4


Mass: 23789.566 Da / Num. of mol.: 2 / Fragment: LIGHT CHAIN (CHAINS L AND A) / Mutation: S25F, P40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody ANTIBODY GERMLINE PRECURSOR TO 28B4


Mass: 23386.072 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN (CHAINS H AND B) / Mutation: V12G, M34F, S35N, V37A, N53K, S76G, D95W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-AAH / 1-[N-4'-NITROBENZYL-N-4'-CARBOXYBUTYLAMINO]METHYLPHOSPHONIC ACID


Mass: 346.273 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N2O7P
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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 100 mM Tris 800 mM NaCl 26% PEG 4000 4 mM hapten, pH 7.5, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
126 %PEG400011
2100 mMTris11pH7.5
3800 mM11NaCl
44 mMhapten11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 19, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 23576 / Num. obs: 20056 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 58.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.39 / Num. unique all: 1960 / % possible all: 91.9
Reflection
*PLUS
Num. measured all: 47152 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 91.9 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS0.4refinement
CCP4(SCALA)data scaling
RefinementResolution: 2.8→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 129832.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1735 9.8 %RANDOM
Rwork0.216 ---
all0.239 20056 --
obs0.223 17787 83.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 12.94 Å2 / ksol: 0.295 e/Å3
Displacement parametersBiso mean: 36.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.72 Å20 Å21.79 Å2
2---2.96 Å20 Å2
3----2.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6638 0 46 0 6684
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 234 9.9 %
Rwork0.324 2140 -
obs--66.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2AAHNV.PARAAHNV.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 9.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Rfactor Rfree: 0.373 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.324

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