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- PDB-4ocx: Fab complex with methotrexate -

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Basic information

Entry
Database: PDB / ID: 4ocx
TitleFab complex with methotrexate
Components
  • Fab ADD056 Heavy Chain
  • Fab ADD056 Light Chain
KeywordsIMMUNE SYSTEM / IgG1/K family
Function / homology
Function and homology information


immune response / extracellular space / metal ion binding
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-MT1 / If kappa light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.39 Å
AuthorsLongenecker, K.L. / Judge, R.A. / Gayda, S. / Manoj, S. / Saldana, S. / Ruan, Q. / Swift, K. / Tetin, S.
CitationJournal: Biochemistry / Year: 2014
Title: Water channel in the binding site of a high affinity anti-methotrexate antibody.
Authors: Gayda, S. / Longenecker, K.L. / Manoj, S. / Judge, R.A. / Saldana, S.C. / Ruan, Q. / Swift, K.M. / Tetin, S.Y.
History
DepositionJan 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab ADD056 Heavy Chain
L: Fab ADD056 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4753
Polymers47,0192
Non-polymers4551
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-22 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.361, 143.361, 143.361
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Antibody Fab ADD056 Heavy Chain


Mass: 23238.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HUMAN EMBRYONIC KIDNEY CELLS / Production host: Homo Sapiens (human)
#2: Antibody Fab ADD056 Light Chain


Mass: 23780.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HUMAN EMBRYONIC KIDNEY CELLS / Production host: Homo Sapiens (human) / References: UniProt: A2NHM3*PLUS
#3: Chemical ChemComp-MT1 / N-(4-{[(2,4-DIAMINOPTERIDIN-1-IUM-6-YL)METHYL](METHYL)AMINO}BENZOYL)-L-GLUTAMIC ACID / METHOTREXATE PROTONATED AT N1


Mass: 455.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N8O5 / Comment: chemotherapy*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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

Crystal growMethod: vapor diffusion / pH: 3.5 / Details: NaCl, citrate pH~3.5, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.39→143.361 Å / Num. all: 38974 / Num. obs: 38974 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 64.9 Å2 / Rsym value: 0.062 / Net I/σ(I): 23.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.39-2.5210.40.5161.55850556100.516100
2.52-2.68100.3232.45342753460.323100
2.68-2.8610.10.19145061150350.191100
2.86-3.0910.40.1116.84856946630.111100
3.09-3.389.90.0769.54293143210.076100
3.38-3.789.20.05811.73613839160.058100
3.78-4.379.70.04813.83352334720.048100
4.37-5.3590.04414.32663129590.044100
5.35-7.579.50.04115.72207123190.041100
7.57-143.36190.03120.21198713330.03199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
BUSTER-TNTBUSTER 2.11.5refinement
PDB_EXTRACT3.14data extraction
JDirectordata collection
XSCALEdata scaling
BUSTER2.11.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→47.2 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.9396 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 1952 5.01 %RANDOM
Rwork0.1869 ---
obs0.1884 38937 99.65 %-
Displacement parametersBiso max: 157.12 Å2 / Biso mean: 52.1956 Å2 / Biso min: 27.02 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.278 Å
Refinement stepCycle: LAST / Resolution: 2.39→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 33 355 3644
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1096SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes65HARMONIC2
X-RAY DIFFRACTIONt_gen_planes501HARMONIC5
X-RAY DIFFRACTIONt_it3397HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion455SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3836SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3397HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4652HARMONIC21.32
X-RAY DIFFRACTIONt_omega_torsion4.1
X-RAY DIFFRACTIONt_other_torsion18.38
LS refinement shellResolution: 2.39→2.45 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2816 160 5.89 %
Rwork0.2288 2556 -
all0.2318 2716 -
obs--99.65 %

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