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- PDB-5ob5: fAb complex with GroBeta. AbVance: increasing our knowledge of an... -

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Basic information

Entry
Database: PDB / ID: 5ob5
TitlefAb complex with GroBeta. AbVance: increasing our knowledge of antibody structural space to enable faster and better decision-making in antibody drug discovery.
Components
  • C-X-C motif chemokine 2
  • fAb Heavy chain
  • fAb Light chain
KeywordsIMMUNE SYSTEM / fAb complex / AbVance project / Pistoia Alliance
Function / homology
Function and homology information


CXCR chemokine receptor binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / Interleukin-10 signaling / neutrophil chemotaxis / response to molecule of bacterial origin / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / G alpha (i) signalling events ...CXCR chemokine receptor binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / Interleukin-10 signaling / neutrophil chemotaxis / response to molecule of bacterial origin / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / G alpha (i) signalling events / cellular response to lipopolysaccharide / inflammatory response / extracellular space / extracellular region
Similarity search - Function
CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 ...CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
C-X-C motif chemokine 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsZhao, B. / Ward, P. / Convery, M.A.
CitationJournal: To Be Published
Title: AbVance: increasing our knowledge of antibody structural space to enable faster and better decision-making in antibody drug discovery
Authors: Convery, M.A.
History
DepositionJun 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-X-C motif chemokine 2
H: fAb Heavy chain
L: fAb Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,62510
Polymers53,9693
Non-polymers6577
Water13,583754
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-64 kcal/mol
Surface area22400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.190, 60.210, 68.250
Angle α, β, γ (deg.)90.00, 110.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-689-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein C-X-C motif chemokine 2 / Growth-regulated protein beta / Gro-beta / Macrophage inflammatory protein 2-alpha / MIP2-alpha


Mass: 6950.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL2, GRO2, GROB, MIP2A, SCYB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P19875

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Antibody , 2 types, 2 molecules HL

#2: Antibody fAb Heavy chain


Mass: 23661.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody fAb Light chain


Mass: 23356.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 3 types, 761 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 754 / 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: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 1.6M ammonium sulfate, 0.5M lithium chloride. 5-30% glycerol added as cryoprotectant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9762 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 70965 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 17.64 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 18.7
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 7047 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
HKL-2000data reduction
SCALEPACKdata scaling
BUSTERphasing
RefinementResolution: 1.65→24.35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.092 / SU Rfree Blow DPI: 0.088 / SU Rfree Cruickshank DPI: 0.083
RfactorNum. reflection% reflectionSelection details
Rfree0.195 4194 5.92 %RANDOM
Rwork0.168 ---
obs0.169 70836 99.7 %-
Displacement parametersBiso mean: 23.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.6279 Å20 Å2-2.3015 Å2
2---2.238 Å20 Å2
3---1.6101 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: 1 / Resolution: 1.65→24.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3779 0 39 754 4572
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014033HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.125504HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1360SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes83HARMONIC2
X-RAY DIFFRACTIONt_gen_planes593HARMONIC5
X-RAY DIFFRACTIONt_it4033HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.22
X-RAY DIFFRACTIONt_other_torsion14.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion533SEMIHARMONIC5
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_contact5319SEMIHARMONIC4
LS refinement shellResolution: 1.65→1.69 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 300 5.81 %
Rwork0.314 4862 -
all0.316 5162 -
obs--99.03 %
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)
14.41270.8260.26550.5906-1.36651.84210.1304-0.05950.30.2066-0.23660.0484-0.21020.53470.1062-0.0986-0.0730.00870.1159-0.0161-0.106211.37634.7346-24.4003
20.4127-0.1313-0.31950.25730.14840.66850.00030.04390.0006-0.0203-0.03170.0216-0.0137-0.01340.03140.001-0.007-0.0093-0.0461-0.0028-0.013-31.26526.6582-15.6675
30.8915-0.0865-0.12290.28180.09760.43530.0042-0.1196-0.01470.0335-0.00960.04510.05640.01320.0054-0.0251-0.005-0.0034-0.03890.0028-0.0395-27.737624.11041.7304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ H|* }
3X-RAY DIFFRACTION3{ L|* }

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