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- PDB-1n7m: Germline 7G12 with N-methylmesoporphyrin -

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Basic information

Entry
Database: PDB / ID: 1n7m
TitleGermline 7G12 with N-methylmesoporphyrin
Components
  • Germline Metal Chelatase Catalytic Antibody, chain H
  • Germline Metal Chelatase Catalytic Antibody, chain L
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
N-METHYLMESOPORPHYRIN / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYin, J. / Andryski, S.E. / Beuscher IV, A.E. / 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 IV, A.E. / Stevens, R.C. / Schultz, P.G.
History
DepositionNov 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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
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

Downloads & links

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Assembly

Deposited unit
H: Germline Metal Chelatase Catalytic Antibody, chain H
L: Germline Metal Chelatase Catalytic Antibody, chain L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9843
Polymers46,4032
Non-polymers5811
Water9,098505
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-24 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.274, 76.236, 60.435
Angle α, β, γ (deg.)90.00, 93.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23334.900 Da / Num. of mol.: 1
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, chain L


Mass: 23067.885 Da / Num. of mol.: 1
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: P01857
#3: Chemical ChemComp-MMP / N-METHYLMESOPORPHYRIN


Mass: 580.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H40N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / 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

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 22% PEG2000MME, 0.2M Ammonium Sulfate, 10mM Cd Sulfate, 1mM NMP, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
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

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→19.79 Å / Num. all: 44580 / Num. obs: 44580 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.8 Å2 / Limit h max: 30 / Limit h min: -30 / Limit k max: 39 / Limit k min: -30 / Limit l max: 31 / Limit l min: 0 / Observed criterion F max: 1427793.72 / Observed criterion F min: 0.32
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Num. obs: 17466 / % possible obs: 95.5 % / Num. measured all: 125917 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 67.9 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 4.9

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.79 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1341 3 %random
Rwork0.22 ---
all-46434 --
obs-44164 95.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 47.204 Å2 / ksol: 0.333298 e/Å3
Displacement parametersBiso max: 78.86 Å2 / Biso mean: 30.79 Å2 / Biso min: 11.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å24.95 Å2
2--3.94 Å20 Å2
3----5.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.13 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3261 0 43 505 3809
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg26.7
X-RAY DIFFRACTIONx_torsion_impr_deg0.78
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 (%)
1.8-1.880.3041452.50.31539040.0255789404969.9
1.88-1.980.2421602.80.24752660.0195795542693.6
1.98-2.10.22717630.22855050.0175786568198.2
2.1-2.270.2281953.40.22655380.0165794573398.9
2.27-2.490.2291582.70.22856110.0185800576999.5
2.49-2.860.2281813.10.22656150.0175808579699.8
2.86-3.590.2311532.60.22656590.0195816581299.9
3.59-19.790.1961732.90.19857250.0155905589899.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.param.parcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4mmp.parmmp.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.203
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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