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- PDB-6obd: Crystal structure of anti-GLD52 Fab complex with human GLD52 pept... -

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Basic information

Entry
Database: PDB / ID: 6obd
TitleCrystal structure of anti-GLD52 Fab complex with human GLD52 peptide mimetic
Components
  • (anti-GLD52 Fab ...) x 2
  • GLD52 peptide mimetic
KeywordsIMMUNE SYSTEM / Fab / GLD52
Function / homology
Function and homology information


: / : / Post-translational modification: synthesis of GPI-anchored proteins / respiratory burst / sperm midpiece / positive regulation of cytosolic calcium ion concentration / extracellular region / membrane / plasma membrane
Similarity search - Function
CAMPATH-1 antigen (CD52) / CAMPATH-1 antigen / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / CAMPATH-1 antigen
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsWei, R.
CitationJournal: Mabs / Year: 2019
Title: Engineering an anti-CD52 antibody for enhanced deamidation stability.
Authors: Qiu, H. / Wei, R. / Jaworski, J. / Boudanova, E. / Hughes, H. / VanPatten, S. / Lund, A. / Day, J. / Zhou, Y. / McSherry, T. / Pan, C.Q. / Sendak, R.
History
DepositionMar 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.2Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: anti-GLD52 Fab light chain
B: anti-GLD52 Fab heavy chain
L: anti-GLD52 Fab light chain
H: anti-GLD52 Fab heavy chain
E: GLD52 peptide mimetic
F: GLD52 peptide mimetic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,05413
Polymers95,4446
Non-polymers6097
Water10,881604
1
A: anti-GLD52 Fab light chain
B: anti-GLD52 Fab heavy chain
E: GLD52 peptide mimetic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0597
Polymers47,7223
Non-polymers3374
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L: anti-GLD52 Fab light chain
H: anti-GLD52 Fab heavy chain
F: GLD52 peptide mimetic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9946
Polymers47,7223
Non-polymers2723
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.400, 131.200, 133.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21A
12H
22B
13E
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114L2 - 216
2114A2 - 216
1124H1 - 213
2124B1 - 213
1134E4 - 12
2134F4 - 12

NCS ensembles :
ID
1
2
3

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Components

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide GLD52 peptide mimetic


Mass: 1022.968 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P31358*PLUS

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Antibody , 2 types, 4 molecules ALBH

#1: Antibody anti-GLD52 Fab light chain


Mass: 23599.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody anti-GLD52 Fab heavy chain


Mass: 23099.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 3 types, 611 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-OPE / PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / COLAMINE PHOSPHORIC ACID / Phosphorylethanolamine


Mass: 141.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H8NO4P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 294 K / Method: evaporation / pH: 5.8 / Details: 0.05M zinc acetate, 17% PEG3350, 0.1M MES pH 5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5419 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.2→30.53 Å / Num. obs: 47509 / % possible obs: 95.9 % / Redundancy: 3.13 % / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.063 / Χ2: 0.94 / Net I/σ(I): 12.9 / Num. measured all: 149992 / Scaling rejects: 1126
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) allΧ2% possible all
2.2-2.281.70.2162.841670.2931.2484.9
2.28-2.3720.1963.142950.2591.1887.9
2.37-2.482.260.1684.145700.2151.1493.8
2.48-2.612.610.1445.247270.1781.1197
2.61-2.772.940.1137.147970.1381.0598.1
2.77-2.993.470.091949050.1070.9999.4
2.99-3.293.990.06812.949210.0780.999.8
3.29-3.764.020.04817.849280.0560.8199.2
3.76-4.733.980.04221.750060.0480.8299.5
4.73-30.533.870.03923.651930.0450.8599.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
d*TREKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30.53 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.869 / SU B: 7.894 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.359 / ESU R Free: 0.28
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3068 2387 5 %RANDOM
Rwork0.2335 ---
obs0.2372 44897 95.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 60.19 Å2 / Biso mean: 28.763 Å2 / Biso min: 12.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2---0.64 Å20 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 2.2→30.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6629 0 21 604 7254
Biso mean--40.08 34.31 -
Num. residues----873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226808
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.9599262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4875865
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.98624.715263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.121151093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7681522
X-RAY DIFFRACTIONr_chiral_restr0.1190.21042
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215102
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1L1645MEDIUM POSITIONAL0.350.5
1L1645MEDIUM THERMAL1.372
2H1567MEDIUM POSITIONAL0.340.5
2H1567MEDIUM THERMAL1.232
3E62MEDIUM POSITIONAL0.510.5
3E62MEDIUM THERMAL1.262
LS refinement shellResolution: 2.199→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 158 -
Rwork0.247 2874 -
all-3032 -
obs--83.34 %

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