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- PDB-1ngy: Chimeric Mature Fab 7g12-Apo -

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Basic information

Entry
Database: PDB / ID: 1ngy
TitleChimeric Mature Fab 7g12-Apo
Components
  • Mature Metal Chelatase Catalytic Antibody, Heavy chain
  • Mature 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: 2.2 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 1.3Oct 16, 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 database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,4882
Polymers46,4882
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-22 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.792, 95.008, 155.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 23374.963 Da / Num. of mol.: 1 / Fragment: 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 Mature Metal Chelatase Catalytic Antibody, Heavy chain


Mass: 23113.029 Da / Num. of mol.: 1 / Fragment: 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.: 146 / 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: 2.35 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 2000MME, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 6.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
127 %PEG2000 MME1drop
2250 mMammonium sulfate1drop
30.5 mMMP1drop
410 mMHEPES1droppH6.6
527 %PEG2000MME1reservoir
6200 mMammonium sulfate1reservoir
7100 mMTris1reservoirpH8.6

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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: 2.2→29.83 Å / Num. all: 22829 / Num. obs: 22829 / Observed criterion σ(F): 0 / Biso Wilson estimate: 26.6 Å2 / Limit h max: 26 / Limit h min: 0 / Limit k max: 43 / Limit k min: 0 / Limit l max: 70 / Limit l min: 0 / Observed criterion F max: 743027.98 / Observed criterion F min: 1.58
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. obs: 22861 / % possible obs: 98.3 % / Num. measured all: 200436 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 97.2 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 10.4

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.82 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1102 4.9 %random
Rwork0.235 ---
all-23199 --
obs-22658 97.7 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 45.0965 Å2 / ksol: 0.363159 e/Å3
Displacement parametersBiso max: 98.71 Å2 / Biso mean: 34.94 Å2 / Biso min: 7.08 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å20 Å20 Å2
2---4.86 Å20 Å2
3---2.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.13 Å
Luzzati d res high-2.2
Refinement stepCycle: LAST / Resolution: 2.2→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3265 0 0 146 3411
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg27.1
X-RAY DIFFRACTIONx_torsion_impr_deg0.81
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 (%)
2.2-2.30.2881314.80.23225930.0252850272495.6
2.3-2.420.3271425.10.25926340.0272882277696.3
2.42-2.570.2921274.50.24826840.0262877281197.7
2.57-2.770.3251234.40.25926690.0292862279297.6
2.77-3.050.3241354.70.26927110.0282886284698.6
3.05-3.490.3211545.40.26727130.0262884286799.4
3.49-4.390.2821404.80.21927550.0242942289598.4
4.39-19.820.1841505.10.19527970.0153035294797.1
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: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.236
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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