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- PDB-4ocy: Fab for methotrexate (unbound apo) -

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Basic information

Entry
Database: PDB / ID: 4ocy
TitleFab for methotrexate (unbound apo)
Components
  • Fab ADD058 Heavy Chain
  • Fab ADD058 Light Chain
KeywordsIMMUNE SYSTEM / IgG1/K family
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
If kappa light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.79 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 ADD058 Heavy Chain
L: Fab ADD058 Light Chain


Theoretical massNumber of molelcules
Total (without water)47,0192
Polymers47,0192
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-22 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.369, 144.369, 144.369
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 ADD058 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 ADD058 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 5.33 Å3/Da / Density % sol: 76.94 %
Crystal growMethod: vapor diffusion / pH: 3.5 / Details: Ammonium sulphate, 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: 2.786→83.351 Å / Num. all: 25192 / Num. obs: 25192 / % possible obs: 99.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 62.78 Å2 / Rsym value: 0.138 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.79-2.9470.541.32555936550.54100
2.94-3.117.20.3622502334590.3699.9
3.11-3.337.30.24232385632680.24299.9
3.33-3.670.1594.52128830300.15999.9
3.6-3.946.90.1255.61936327960.12599.7
3.94-4.47.30.1026.41853725310.10299.8
4.4-5.097.10.0926.81595522500.09299.5
5.09-6.236.80.0986.51293118910.09898.8
6.23-8.817.20.0936.71067614790.09398.4
8.81-83.3516.60.0786.954698330.07897.2

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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: 2.79→25.47 Å / Cor.coef. Fo:Fc: 0.9243 / Cor.coef. Fo:Fc free: 0.9089 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 1275 5.09 %RANDOM
Rwork0.1822 ---
obs0.1835 25038 99.35 %-
Displacement parametersBiso max: 118.1 Å2 / Biso mean: 41.7703 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.279 Å
Refinement stepCycle: LAST / Resolution: 2.79→25.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3266 0 0 215 3481
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1089SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes65HARMONIC2
X-RAY DIFFRACTIONt_gen_planes487HARMONIC5
X-RAY DIFFRACTIONt_it3353HARMONIC20
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_contact3669SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3353HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4578HARMONIC21.3
X-RAY DIFFRACTIONt_omega_torsion3.88
X-RAY DIFFRACTIONt_other_torsion19.62
LS refinement shellResolution: 2.79→2.9 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2492 143 5.05 %
Rwork0.1971 2687 -
all0.1997 2830 -
obs--99.35 %

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