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- PDB-1ngz: Chimeric Germline Fab 7g12-apo -

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Basic information

Entry
Database: PDB / ID: 1ngz
TitleChimeric Germline Fab 7g12-apo
Components
  • Germline Metal Chelatase Catalytic Antibody, Heavy chain
  • Germline Metal Chelatase Catalytic Antibody, Light chain
KeywordsIMMUNE SYSTEM / antibody / immunoglobulin / antigen binding fragment (Fab)
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYin, J. / Andryski, S.A. / Beuscher, A.B. / Stevens, R.C. / Schultz, P.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Structural evidence for substrate strain in antibody catalysis
Authors: Yin, J. / Andryski, S.A. / Beuscher, A.B. / Stevens, R.C. / Schultz, P.G.
History
DepositionDec 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE The gene sequences are derived from a mouse hybridoma. The sequences of the protein chains ...SEQUENCE The gene sequences are derived from a mouse hybridoma. The sequences of the protein chains are not found in any sequence databases.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Germline Metal Chelatase Catalytic Antibody, Light chain
B: Germline Metal Chelatase Catalytic Antibody, Heavy chain


Theoretical massNumber of molelcules
Total (without water)46,8512
Polymers46,8512
Non-polymers00
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-20 kcal/mol
Surface area20360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.874, 44.416, 57.863
Angle α, β, γ (deg.)84.22, 77.04, 89.39
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Germline Metal Chelatase Catalytic Antibody, Light chain


Mass: 23334.900 Da / Num. of mol.: 1 / Fragment: germline Fab fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Production host: Escherichia coli (E. coli) / References: UniProt: Q58EU4
#2: Antibody Germline Metal Chelatase Catalytic Antibody, Heavy chain


Mass: 23516.400 Da / Num. of mol.: 1 / Fragment: germline Fab fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 1.84 Å3/Da / Density % sol: 32.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG2000 MME, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
122 %PEG2000 MME1drop
2200 mM1dropLiCl
3100 mMsodium citrate1droppH4.0
424 %PEG2000 MME1reservoir
5200 mMammonium acetate1reservoir
610 mMcadmium sulfate1reservoir
71 mMNMP1reservoir
8100 mMsodium acetate1reservoirpH4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→28.94 Å / Num. all: 44964 / Num. obs: 44964 / Observed criterion σ(F): 0 / Biso Wilson estimate: 15.9 Å2 / Limit h max: 23 / Limit h min: -23 / Limit k max: 27 / Limit k min: -23 / Limit l max: 36 / Limit l min: 0 / Observed criterion F max: 1362450.56 / Observed criterion F min: 1
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / % possible obs: 91.2 % / Num. measured all: 97524 / Rmerge(I) obs: 0.034
Reflection shell
*PLUS
% possible obs: 81.9 % / Rmerge(I) obs: 0.112 / Mean I/σ(I) obs: 6.7

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→19.88 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2236 5 %random
Rwork0.207 ---
all-49422 --
obs-44654 90.4 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 36.0425 Å2 / ksol: 0.366482 e/Å3
Displacement parametersBiso max: 60.01 Å2 / Biso mean: 14.77 Å2 / Biso min: 3.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å2-1.56 Å20.27 Å2
2--0.45 Å20.49 Å2
3----0.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.03 Å
Luzzati d res high-1.6
Refinement stepCycle: LAST / Resolution: 1.6→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 0 462 3753
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg26.8
X-RAY DIFFRACTIONx_torsion_impr_deg0.82
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.6-1.670.322495.20.29745710.026187482077.9
1.67-1.760.2552745.10.22550850.0156225535986.1
1.76-1.870.24827250.20552050.0156182547788.6
1.87-2.020.2422704.80.19753030.0156166557390.4
2.02-2.220.2272744.80.254500.0146196572492.4
2.22-2.540.2392824.90.21355060.0146158578894
2.54-3.20.2383015.10.21356280.0146191592995.8
3.2-19.880.2093145.20.1956700.0126172598497
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg

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