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- PDB-1ngw: Chimeric Affinity Matured Fab 7g12 complexed with mesoporphyrin -

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Basic information

Entry
Database: PDB / ID: 1ngw
TitleChimeric Affinity Matured Fab 7g12 complexed with mesoporphyrin
Components
  • Mature Metal Chelatase Catalytic Antibody, Heavy chain
  • Mature Metal Chelatase Catalytic Antibody, Light chain
KeywordsIMMUNE SYSTEM / antibody / immunoglobulin / antigen binding fragment
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-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 / Ig heavy chain V region 1-72
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 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
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 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 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 databases.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)94,2206
Polymers93,0584
Non-polymers1,1612
Water45025
1
L: Mature Metal Chelatase Catalytic Antibody, Light chain
H: Mature Metal Chelatase Catalytic Antibody, Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1103
Polymers46,5292
Non-polymers5811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-26 kcal/mol
Surface area19100 Å2
MethodPISA
2
A: Mature Metal Chelatase Catalytic Antibody, Light chain
B: Mature Metal Chelatase Catalytic Antibody, Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1103
Polymers46,5292
Non-polymers5811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-25 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.721, 134.215, 72.951
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 23432.014 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 Mature Metal Chelatase Catalytic Antibody, Heavy chain


Mass: 23097.074 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) / References: UniProt: P06328
#3: Chemical ChemComp-MMP / N-METHYLMESOPORPHYRIN


Mass: 580.716 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H40N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.65 Å3/Da / Density % sol: 53.22 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: PEG2000MME, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 100K
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: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20.15 Å / Num. all: 38586 / Num. obs: 38586 / Observed criterion σ(F): 0 / Biso Wilson estimate: 14.9 Å2 / Limit h max: 41 / Limit h min: 0 / Limit k max: 55 / Limit k min: 0 / Limit l max: 30 / Limit l min: 0 / Observed criterion F max: 360138.7 / Observed criterion F min: 0.32
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. obs: 28954 / % possible obs: 98.7 % / Num. measured all: 140870 / Rmerge(I) obs: 0.108
Reflection shell
*PLUS
% possible obs: 97.7 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 4.8

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MIR / Resolution: 2.6→19.92 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.318 1379 5 %random
Rwork0.275 ---
all-31071 --
obs-27646 89 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 27.1555 Å2 / ksol: 0.272359 e/Å3
Displacement parametersBiso max: 150.07 Å2 / Biso mean: 59.31 Å2 / Biso min: 4.03 Å2
Baniso -1Baniso -2Baniso -3
1--9.53 Å20 Å20 Å2
2--0.37 Å20 Å2
3---9.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.65 Å0.52 Å
Luzzati d res low-5 Å
Luzzati sigma a1.21 Å0.68 Å
Luzzati d res high-2.6
Refinement stepCycle: LAST / Resolution: 2.6→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6536 0 84 25 6645
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg26.5
X-RAY DIFFRACTIONx_torsion_impr_deg0.89
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 (%)
2.6-2.720.6611234.90.624020.063842252565.7
2.72-2.860.4751745.50.46130160.0363824319083.4
2.86-3.040.4011544.50.34732780.0323856343289
3.04-3.270.3791794.90.28934460.0283837362594.5
3.27-3.60.3721835.20.32233130.0273841349691
3.6-4.120.3791915.50.3432860.0273895347789.3
4.12-5.170.2191834.70.17236720.0163928385598.1
5.17-19.920.2721924.70.20538540.024080404699.2
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 DIFFRACTION4mmp.parmmp.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.3 / Rfactor Rwork: 0.264
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
LS refinement shell
*PLUS
Rfactor Rfree: 0.661 / Rfactor Rwork: 0.6

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