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- PDB-1ngx: Chimeric Germline Fab 7g12 with jeffamine fragment bound -

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Basic information

Entry
Database: PDB / ID: 1ngx
TitleChimeric Germline Fab 7g12 with jeffamine fragment bound
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 / Chem-JEF
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYin, J. / Andryski, S.E. / 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.E. / Beuscher, A.B. / Stevens, R.C. / Schultz, P.G.
History
DepositionDec 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
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.
Remark 600HETEROGEN THE JEF RESIDUE PRESENT IN THE COORDINATES IS ONLY A FRAGMENT OF THE LARGER JEFFAMINE ...HETEROGEN THE JEF RESIDUE PRESENT IN THE COORDINATES IS ONLY A FRAGMENT OF THE LARGER JEFFAMINE POLYMER. IT DOES NOT CONTAIN ATOMS FROM EITHER TERMINI OF THIS POLYMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Germline Metal Chelatase Catalytic Antibody, Light chain
B: Germline Metal Chelatase Catalytic Antibody, Heavy chain
L: Germline Metal Chelatase Catalytic Antibody, Light chain
H: Germline Metal Chelatase Catalytic Antibody, Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0836
Polymers92,8884
Non-polymers1,1962
Water12,106672
1
A: Germline Metal Chelatase Catalytic Antibody, Light chain
B: Germline Metal Chelatase Catalytic Antibody, Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0423
Polymers46,4442
Non-polymers5981
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-20 kcal/mol
Surface area19490 Å2
MethodPISA
2
L: Germline Metal Chelatase Catalytic Antibody, Light chain
H: Germline Metal Chelatase Catalytic Antibody, Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0423
Polymers46,4442
Non-polymers5981
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-18 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.666, 64.723, 93.382
Angle α, β, γ (deg.)90.00, 92.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23391.951 Da / Num. of mol.: 2 / 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)
#2: Antibody Germline Metal Chelatase Catalytic Antibody, Heavy chain


Mass: 23051.930 Da / Num. of mol.: 2 / 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: Chemical ChemComp-JEF / O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) / JEFFAMINE


Mass: 597.822 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H63NO10
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 40.97 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: PEG2000MME, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 100K

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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: 1.7→26.42 Å / Num. all: 87547 / Num. obs: 87547 / Observed criterion σ(F): 0 / Biso Wilson estimate: 15 Å2 / Limit h max: 41 / Limit h min: -41 / Limit k max: 35 / Limit k min: -41 / Limit l max: 54 / Limit l min: 0 / Observed criterion F max: 602326.14 / Observed criterion F min: 0.32

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.87 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25 3696 5 %random
Rwork0.225 ---
all-78130 --
obs-73191 93.7 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 32.8053 Å2 / ksol: 0.327777 e/Å3
Displacement parametersBiso max: 77.66 Å2 / Biso mean: 22.1 Å2 / Biso min: 5.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.68 Å20 Å21.95 Å2
2--2.21 Å20 Å2
3---0.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.06 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6528 0 56 672 7256
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg27
X-RAY DIFFRACTIONx_torsion_impr_deg0.8
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 (%)
1.8-1.880.29942750.26781290.0149707855688.1
1.88-1.980.2694615.30.22882500.0139714871189.7
1.98-2.10.2464274.80.21684010.0129751882890.5
2.1-2.270.25744650.21785270.0129760897391.9
2.27-2.490.25145650.23187440.0129751920094.3
2.49-2.860.2544815.10.24189850.0129775946696.8
2.86-3.590.2594905.10.23491140.0129825960497.8
3.59-19.870.2295085.20.20693450.019948985399
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4eth.pareth.top

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