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- PDB-3qpx: Crystal structure of Fab C2507 -

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Basic information

Entry
Database: PDB / ID: 3qpx
TitleCrystal structure of Fab C2507
Components
  • Fab C2507 heavy chain
  • Fab C2507 light chain
KeywordsIMMUNE SYSTEM / immunoglobulin / mouse IL-17A
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLuo, J. / Teplyakov, A. / Obmolova, O. / Malia, T. / Gilliland, G.L.
CitationJournal: To be Published
Title: Crystal structure of Fab C2507
Authors: Luo, J. / Teplyakov, A. / Obmolova, O. / Malia, T. / Gilliland, G.L.
History
DepositionFeb 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab C2507 light chain
H: Fab C2507 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,48730
Polymers47,7992
Non-polymers2,68828
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-197 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.150, 87.050, 100.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody Fab C2507 light chain


Mass: 23575.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Rattus norvegicus / Cell line (production host): HEK293 / Production host: homo sapiens (human)
#2: Antibody Fab C2507 heavy chain


Mass: 24224.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Rattus norvegicus / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Non-polymers , 5 types, 450 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.9 M (NH4)2SO4, 50 mM CdCl2, 0.1 M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 7, 2008 / Details: Osmic VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→66 Å / Num. all: 35233 / Num. obs: 35233 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.098

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
PHENIX(phenix.refine)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→43.525 Å / SU ML: 0.25 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 1753 4.99 %Random
Rwork0.2246 ---
obs0.2266 35106 96.69 %-
all-35106 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 76.696 Å2 / ksol: 0.417 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.1221 Å2-0 Å20 Å2
2---3.586 Å20 Å2
3---1.4639 Å2
Refinement stepCycle: LAST / Resolution: 2→43.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 122 422 3904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053557
X-RAY DIFFRACTIONf_angle_d0.974824
X-RAY DIFFRACTIONf_dihedral_angle_d16.7761246
X-RAY DIFFRACTIONf_chiral_restr0.067528
X-RAY DIFFRACTIONf_plane_restr0.004607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05410.36471220.29162494X-RAY DIFFRACTION95
2.0541-2.11450.30981170.26592509X-RAY DIFFRACTION96
2.1145-2.18280.2731380.24452493X-RAY DIFFRACTION96
2.1828-2.26080.28821260.23742486X-RAY DIFFRACTION96
2.2608-2.35130.31451400.24982558X-RAY DIFFRACTION96
2.3513-2.45830.32521350.25332543X-RAY DIFFRACTION97
2.4583-2.58790.3111350.2612544X-RAY DIFFRACTION97
2.5879-2.750.35421510.2552575X-RAY DIFFRACTION98
2.75-2.96230.32071330.24382593X-RAY DIFFRACTION98
2.9623-3.26030.28471510.22462622X-RAY DIFFRACTION99
3.2603-3.73190.23981200.18322675X-RAY DIFFRACTION99
3.7319-4.70090.1891490.15552616X-RAY DIFFRACTION97
4.7009-43.53530.1941360.19422645X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0770.0389-0.08531.05650.15850.67560.00170.02850.0298-0.13010.02560.0349-0.0598-0.0316-0.03940.2292-0.02170.00030.20920.00630.2352-1.465211.8485-26.4653
20.5952-0.2678-0.03170.40220.39730.67250.0433-0.11650.0426-0.00680.0759-0.13170.01430.0432-0.10250.27670.0006-0.00210.2961-0.0420.2655-2.019730.83616.2119
30.1406-0.423-0.13331.38950.27180.6271-0.0537-0.0581-0.09960.03120.08030.09420.10720.06930.00050.24790.00110.0240.24450.01390.2588-2.031-6.0664-12.2431
40.5753-0.1874-0.62570.51270.6730.67110.0013-0.14140.11040.25910.04440.0240.1175-0.0369-0.03390.2965-0.0045-0.00140.288-0.00860.2445-9.555617.49126.2785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain L and resid 1:108
2X-RAY DIFFRACTION2chain L and resid 109:213
3X-RAY DIFFRACTION3chain H and resid 1:119
4X-RAY DIFFRACTION4chain H and resid 120:222

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