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- PDB-1fl5: THE UNLIGANDED GERMLINE PRECURSOR TO THE SULFIDE OXIDASE CATALYTI... -

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Basic information

Entry
Database: PDB / ID: 1fl5
TitleTHE UNLIGANDED GERMLINE PRECURSOR TO THE SULFIDE OXIDASE CATALYTIC ANTIBODY 28B4.
Components(ANTIBODY GERMLINE PRECURSOR TO ANTIBODY 28B4) x 2
KeywordsIMMUNE SYSTEM / catalytic antibody / germline antibody / sulfide oxidase
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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 1.3Oct 30, 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 ANTIBODY 28B4
H: ANTIBODY GERMLINE PRECURSOR TO ANTIBODY 28B4
A: ANTIBODY GERMLINE PRECURSOR TO ANTIBODY 28B4
B: ANTIBODY GERMLINE PRECURSOR TO ANTIBODY 28B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5436
Polymers94,3514
Non-polymers1922
Water4,936274
1
L: ANTIBODY GERMLINE PRECURSOR TO ANTIBODY 28B4
H: ANTIBODY GERMLINE PRECURSOR TO ANTIBODY 28B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2723
Polymers47,1762
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-32 kcal/mol
Surface area19680 Å2
MethodPISA
2
A: ANTIBODY GERMLINE PRECURSOR TO ANTIBODY 28B4
B: ANTIBODY GERMLINE PRECURSOR TO ANTIBODY 28B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2723
Polymers47,1762
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-34 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.420, 69.650, 85.310
Angle α, β, γ (deg.)74.56, 80.18, 77.55
Int Tables number1
Space group name H-MP1
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 ANTIBODY 28B4 / IF KAPPA LIGHT CHAIN


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 ANTIBODY 28B4 / IGG1 HEAVY CHAIN


Mass: 23386.072 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN (CHAINS H AND B) / Mutation: V12G, M34F, S35N, V37A, N53L, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 3.9
Details: 100 mM ammonium sulfate 50 mM sodium acetate 10% PEG 2000 MME, pH 3.9, VAPOR DIFFUSION, temperature 277.0K
Crystal grow
*PLUS
Temperature: 100 K / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMammonium sulfate11
250 mMsodium acetate11pH3.9
310 %PEG MME200011

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 51231 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 18
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 2 % / Rmerge(I) obs: 0.221 / Num. unique all: 4849 / % possible all: 70.5
Reflection
*PLUS
Num. measured all: 109371
Reflection shell
*PLUS
Highest resolution: 2.07 Å / Lowest resolution: 2.15 Å / % possible obs: 95.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementResolution: 2.1→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 376700.18 / 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
Rfree0.268 4037 10.1 %RANDOM
Rwork0.226 ---
all0.238 51239 --
obs0.233 39790 87 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.89 Å2 / ksol: 0.298 e/Å3
Displacement parametersBiso mean: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.05 Å2-0.26 Å2-3.87 Å2
2---8.55 Å22.95 Å2
3---5.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6638 0 10 274 6922
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_improper_angle_d1.03
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 542 10.1 %
Rwork0.256 4849 -
obs--70.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAWATER_REP.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.1 % / Rfactor obs: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03
LS refinement shell
*PLUS
Rfactor Rfree: 0.318 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.256

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