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- PDB-9gp2: apoJ22.9 Unliganded structure of an Fab fragment from the therape... -

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Basic information

Entry
Database: PDB / ID: 9gp2
TitleapoJ22.9 Unliganded structure of an Fab fragment from the therapeutic antibody J22.9-xi
Components
  • Chains: H
  • Chains: L
KeywordsANTITUMOR PROTEIN / Fab fragment / therapeutic antibody / chimeric antibody
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMarino, S.F. / Daumke, O.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: To Be Published
Title: apoJ22.9 Unliganded structure of an Fab fragment from the therapeutic antibody J22.9-xi
Authors: Marino, S.F. / Daumke, O.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionSep 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Chains: H
L: Chains: L


Theoretical massNumber of molelcules
Total (without water)47,2582
Polymers47,2582
Non-polymers00
Water10,557586
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-23 kcal/mol
Surface area19840 Å2
Unit cell
Length a, b, c (Å)122.374, 122.374, 170.125
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11H-527-

HOH

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Components

#1: Antibody Chains: H


Mass: 23786.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fab heavy chain sequence / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Chains: L


Mass: 23471.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fab light chain sequence / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.89 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: BisTris PEG 3350 CuCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.968→49.67 Å / Num. obs: 53707 / % possible obs: 99.73 % / Redundancy: 10.8 % / Biso Wilson estimate: 32.52 Å2 / Rrim(I) all: 0.1 / Net I/σ(I): 17.59
Reflection shellResolution: 1.97→2 Å / Mean I/σ(I) obs: 2.07 / Num. unique obs: 2688 / Rrim(I) all: 1

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Processing

Software
NameVersionClassification
PHENIXdev_5407refinement
XDSVERSION March 30, 2013data reduction
XDSVERSION March 30, 2013data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→49.67 Å / SU ML: 0.2159 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.6956
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2021 2687 5 %
Rwork0.1615 51020 -
obs0.1635 53707 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.5 Å2
Refinement stepCycle: LAST / Resolution: 1.97→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 0 586 3907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013408
X-RAY DIFFRACTIONf_angle_d1.03094632
X-RAY DIFFRACTIONf_chiral_restr0.0607519
X-RAY DIFFRACTIONf_plane_restr0.0088595
X-RAY DIFFRACTIONf_dihedral_angle_d17.42661234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-20.34611340.29292554X-RAY DIFFRACTION96.34
2-2.040.25881390.25732640X-RAY DIFFRACTION99.82
2.04-2.080.26391380.23242615X-RAY DIFFRACTION99.75
2.08-2.130.21381400.20362645X-RAY DIFFRACTION99.75
2.13-2.180.24751390.20112645X-RAY DIFFRACTION99.82
2.18-2.230.27381400.18732647X-RAY DIFFRACTION99.93
2.23-2.290.27421390.21662639X-RAY DIFFRACTION99.78
2.29-2.360.23371400.18142672X-RAY DIFFRACTION99.93
2.36-2.440.26841400.17432660X-RAY DIFFRACTION100
2.44-2.520.2231400.17672658X-RAY DIFFRACTION99.93
2.52-2.630.23061410.16692665X-RAY DIFFRACTION99.96
2.63-2.740.24311400.16672679X-RAY DIFFRACTION100
2.74-2.890.21121420.15282688X-RAY DIFFRACTION100
2.89-3.070.22511420.15682702X-RAY DIFFRACTION100
3.07-3.310.1811420.15492703X-RAY DIFFRACTION100
3.31-3.640.15851440.13872718X-RAY DIFFRACTION100
3.64-4.170.15741440.13332740X-RAY DIFFRACTION100
4.17-5.250.16171470.11932788X-RAY DIFFRACTION100
5.25-49.670.20811560.17792962X-RAY DIFFRACTION99.9
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.67675313798-1.59920847271-4.230706829681.508096729012.791517120775.71345758468-0.025886341151-0.3742776805270.3936603579840.2363711191410.097474431537-0.117020497375-0.8015264983740.217037503209-0.245415566690.4611566494880.155549397912-0.0529833900120.3407288973230.02090425662770.40528822446963.4910511463-7.0288404096832.259161534
23.59964664234-1.556256280382.972624674992.78610584224-1.51261879262.47819268795-0.552762064559-1.035629273140.4977640350410.5295814761060.562855429657-0.0283554843594-0.972950087298-0.759541755293-0.05312593750280.6187014024580.235183240499-0.07422443347810.449253471612-0.08910287751660.44021384717864.9381215853-8.6644272075845.8300251174
32.66537331744-0.3444366525051.836388436272.96786223612-1.455724138542.94282856009-0.164537242633-0.122805349710.335773340370.204887324643-0.0666284516554-0.34555653905-0.1819982371450.1851277919750.1529463708420.4225808710070.123434243877-0.02530939998250.3146306857180.0004163748233430.400176235469.8483358-14.924650596638.1151511212
40.727307467910.08051313737450.7063724956610.3808986637640.3909147319120.946512726835-0.220802161829-0.2210561978970.09523798774810.09874928291270.100332108764-0.115532177439-0.0940146200481-0.106914554640.1351620756970.3644878240950.101366897176-0.005983078721270.2698258157030.0204065241530.3331857213458.2376777509-10.559213658823.1072518164
56.95156862089-0.0431142870025-0.2462505838643.27213982946-0.5824430153434.54718221676-0.1243124138560.753122849977-0.100278479993-0.266692434560.09160757981990.9821790345330.190275416945-0.9264020633790.003748947136060.384478619801-0.00444277079841-0.05999639641740.451431707714-0.02618066758670.58387531542838.165235562-15.00725848297.43814554084
65.952042142060.3504802944460.1905910880772.286281081720.430180004111.974092572980.111500690048-0.1026923900330.1746625029840.0276409058284-0.2029148452720.407287430452-0.0149665844172-0.483509533570.05438267950610.239974619780.00959873078310.01807331851080.235848524362-0.02408113752210.26057410921543.9068454989-10.410196056215.2705241149
73.859269685151.414037952280.1356913919883.553758225381.072450482041.57043885393-0.4528401804340.4358120615180.702963098471-0.7826036872210.0399494750560.825485398687-0.599828107245-0.3661729545660.3599724063230.3655371367430.0736728122408-0.1001222425270.296856197245-0.0271272850340.37613884508741.1573264856-3.644652062957.90162137988
86.69264533248-1.885702959621.031033288971.517581255650.4940274318943.01865925072-0.1180943577120.337976239543-0.214444818921-0.108254227230.2353876208390.01712602566410.573514724627-0.331177541214-0.05610871747710.530477800592-0.0394043322766-0.0008703994332120.4433617918940.1133187408340.39860431652453.0327481242-35.162144226434.2621143954
95.284081146290.7593931042520.9447828776591.710360653640.275707088263.827150617120.118305960577-0.572122231951-0.1820641158460.1505987860320.01153782637120.1230169535230.18122694677-0.791240689357-0.1041413387460.4172112869570.03050932243350.02316417182650.5147420849850.1080555846290.31632219043354.3026709482-30.083817340442.4819642648
108.359063397460.6861903736615.825049068250.1644576882590.5549648719384.344434072520.0852848735217-0.16945877326-0.59664546119-0.01925881711420.142950812356-0.02233525888770.409271816966-0.299474815849-0.2472380675550.376135669513-0.0103851596467-0.0008608030170760.292573290130.07254827868390.27446177589653.6164755092-30.299932336132.8238089493
112.911576887260.48963450879-0.7047715486281.355403275750.02387170348786.131170786020.071815660145-0.007340464367450.00286057902568-0.00816200827884-0.02558708603320.08053412321590.125871367927-0.126246845815-0.03096863143680.312744935969-0.0464821610132-0.04945394954140.266876228068-0.01753182244260.31105396375946.0479437032-23.62807151496.20813046442
122.481859846180.679669304364-1.525210014661.82799258978-1.447889632924.10697446595-0.03973985974960.0644091165608-0.158686411856-0.1831969526920.06105921174870.213974914950.449908102696-0.441473582056-0.04550580536320.372803421182-0.0797925101525-0.04290857836490.323382598651-0.01738022569520.33398198005743.1443942105-25.22362216385.5990929566
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 17 )HA1 - 171 - 17
22chain 'H' and (resid 18 through 33 )HA18 - 3318 - 33
33chain 'H' and (resid 34 through 106 )HA34 - 10634 - 106
44chain 'H' and (resid 107 through 131 )HA107 - 131107 - 131
55chain 'H' and (resid 132 through 152 )HA132 - 152132 - 152
66chain 'H' and (resid 153 through 210 )HA153 - 210153 - 210
77chain 'H' and (resid 211 through 222 )HA211 - 222211 - 222
88chain 'L' and (resid 1 through 18 )LB1 - 181 - 18
99chain 'L' and (resid 19 through 90 )LB19 - 9019 - 90
1010chain 'L' and (resid 91 through 113 )LB91 - 11391 - 113
1111chain 'L' and (resid 114 through 163 )LB114 - 163114 - 163
1212chain 'L' and (resid 164 through 213 )LB164 - 213164 - 213

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