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- PDB-6ks2: Structure of anti-Ghrelin receptor antibody -

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Basic information

Entry
Database: PDB / ID: 6ks2
TitleStructure of anti-Ghrelin receptor antibody
Components
  • Fab7881 Heavy Chain (FabH)
  • Fab7881 Light Chain (FabL)
KeywordsIMMUNE SYSTEM / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.753 Å
AuthorsShiimura, Y. / Horita, S. / Asada, H. / Hirata, K. / Iwata, S. / Kojima, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Nat Commun / Year: 2020
Title: Structure of an antagonist-bound ghrelin receptor reveals possible ghrelin recognition mode.
Authors: Shiimura, Y. / Horita, S. / Hamamoto, A. / Asada, H. / Hirata, K. / Tanaka, M. / Mori, K. / Uemura, T. / Kobayashi, T. / Iwata, S. / Kojima, M.
History
DepositionAug 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 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
A: Fab7881 Light Chain (FabL)
B: Fab7881 Heavy Chain (FabH)
C: Fab7881 Light Chain (FabL)
D: Fab7881 Heavy Chain (FabH)


Theoretical massNumber of molelcules
Total (without water)95,2224
Polymers95,2224
Non-polymers00
Water11,169620
1
A: Fab7881 Light Chain (FabL)
B: Fab7881 Heavy Chain (FabH)


Theoretical massNumber of molelcules
Total (without water)47,6112
Polymers47,6112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-23 kcal/mol
Surface area19240 Å2
MethodPISA
2
C: Fab7881 Light Chain (FabL)
D: Fab7881 Heavy Chain (FabH)


Theoretical massNumber of molelcules
Total (without water)47,6112
Polymers47,6112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-23 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.239, 107.916, 189.892
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab7881 Light Chain (FabL)


Mass: 24278.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab7881 Heavy Chain (FabH)


Mass: 23331.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM BICINE pH 9.0, 100mM Sodium Chloride, 30%(v/v) PEG550MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→47.473 Å / Num. obs: 169522 / % possible obs: 99.08 % / Redundancy: 3.53 % / Biso Wilson estimate: 28.39 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.062 / Net I/σ(I): 6.7
Reflection shellResolution: 1.74→1.81 Å / Redundancy: 3.54 % / Rmerge(I) obs: 1.196 / Num. unique obs: 16885 / CC1/2: 0.498 / Rpim(I) all: 0.74 / % possible all: 98.66

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2210refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q9K

1q9k


Resolution: 1.753→47.473 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.71
RfactorNum. reflection% reflection
Rfree0.2328 4345 4.96 %
Rwork0.1922 --
obs0.1942 87517 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.77 Å2 / Biso mean: 40.0923 Å2 / Biso min: 14.96 Å2
Refinement stepCycle: final / Resolution: 1.753→47.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6570 0 0 620 7190
Biso mean---42.35 -
Num. residues----872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116855
X-RAY DIFFRACTIONf_angle_d1.2159400
X-RAY DIFFRACTIONf_chiral_restr0.0711094
X-RAY DIFFRACTIONf_plane_restr0.0081185
X-RAY DIFFRACTIONf_dihedral_angle_d14.7574159
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7535-1.77340.3361290.2963249290
1.7734-1.79430.35751250.30232717100
1.7943-1.81620.34521460.3005274599
1.8162-1.83910.3371530.2893272097
1.8391-1.86330.35821390.27642693100
1.8633-1.88890.32471630.27892748100
1.8889-1.91590.30531460.2766273398
1.9159-1.94450.3371420.2838271399
1.9445-1.97480.33531550.28272717100
1.9748-2.00720.36751340.2986279399
2.0072-2.04180.34451570.2778271999
2.0418-2.0790.28511360.25082770100
2.079-2.11890.27161450.2224274199
2.1189-2.16220.28091350.21562751100
2.1622-2.20920.26781540.21212778100
2.2092-2.26060.26741310.2077275399
2.2606-2.31710.27841570.20472790100
2.3171-2.37980.25781560.2068272899
2.3798-2.44980.25691330.20152813100
2.4498-2.52890.26221580.20392762100
2.5289-2.61920.24311400.2042789100
2.6192-2.72410.25391280.19362798100
2.7241-2.84810.27521390.19782831100
2.8481-2.99820.2171440.19872816100
2.9982-3.1860.22591400.1904277899
3.186-3.43190.20221510.18142806100
3.4319-3.77720.20641370.16252874100
3.7772-4.32340.16951560.14992850100
4.3234-5.44580.16851510.12922910100
5.4458-47.4730.17761650.16223044100
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)
10.4565-0.1445-0.01952.48720.25213.6264-0.0182-0.2087-0.07781.36460.0008-0.2040.6287-0.17590.00720.92330.0189-0.08990.34940.00780.2844-13.7588-3.036113.1983
21.5763-0.1852-1.6552.81772.7326.47210.0979-0.12250.01720.47780.08-0.1780.24310.2379-0.11040.2953-0.0179-0.00550.2094-0.01270.2478-12.1521-17.4583-20.9815
32.0350.241-1.80562.83780.22697.53570.075-0.036-0.29230.60180.04210.14721.34650.4307-0.00570.43160.0350.00520.2156-0.01190.2803-12.955-26.7506-24.3134
40.17050.48350.63855.13070.62334.15830.03640.39660.1011-0.53040.1514-0.3736-0.906-0.067-0.16210.4436-0.0140.02160.2669-0.02240.2758-13.281213.3765-9.378
55.0033-2.0395-0.99365.59242.39965.7087-0.1344-0.2244-0.04530.25550.08090.3313-0.5007-0.3450.01910.39340.0404-0.0210.24250.01690.2859-17.141916.30371.6505
63.84330.1182-0.41056.46843.18485.3560.0094-0.09020.41680.24830.3405-1.0258-0.50990.4875-0.35740.4123-0.0603-0.08510.3148-0.03510.3715-7.001216.36893.7349
71.56722.42120.87973.79140.82074.67850.0110.04530.3361-0.36290.3515-0.9381-0.92120.225-0.23780.5125-0.0753-0.00110.2618-0.01240.3786-8.718917.6209-5.3309
81.1752-0.44011.2395.53732.18575.5312-0.1215-0.11590.0080.29250.319-0.2079-0.1407-0.0113-0.17570.27330.0097-0.01340.16980.01680.2814-14.98929.3602-3.1676
98.83711.8521-0.18452.69660.86438.8585-0.08380.1853-0.7779-0.02760.52180.10840.7586-0.6412-0.32680.2907-0.0572-0.02170.3779-0.03620.3938-24.0391-16.2386-25.7299
103.57792.90520.5638.75242.28443.6448-0.0563-0.115-0.0846-0.1718-0.17970.45670.0826-0.42690.1760.2139-0.00210.01610.2416-0.01980.2603-20.1166-5.3858-17.9769
111.0755-1.26341.98896.84641.38476.27030.04140.2492-0.35320.3898-0.1099-0.41650.4873-0.20.12390.3152-0.03980.01990.2633-0.00230.2637-17.0795-8.2973-14.3169
123.56081.8508-0.0296.519-0.11033.5949-0.08120.0848-0.3317-0.1275-0.07170.5630.2029-0.80840.07670.2592-0.05620.03190.4137-0.10880.3007-25.3051-8.6003-19.0213
131.6289-1.0711-0.66766.42692.87511.7967-0.0060.1445-0.0532-0.8419-0.20790.663-0.3608-0.35940.24350.38050.0477-0.09410.5073-0.07610.3884-26.8738-5.3785-25.2922
142.47460.0421-0.37524.6403-0.78753.09430.0928-0.0571-0.13490.2446-0.07560.10970.2783-0.0552-0.00080.2834-0.03420.05420.26050.03360.2625-24.189819.7777-28.0731
151.6095-1.6771-1.31522.21871.70081.216-0.128-0.0826-0.17250.20840.0390.04260.20230.0370.08870.31230.02380.07250.20840.01630.30231.65258.1784-48.6536
169.82860.95630.58430.6836-0.70540.34310.10280.805-0.2486-0.00170.0397-0.07990.04890.1413-0.01780.1358-0.00280.01940.2701-0.0250.2845-8.830238.8205-44.1295
175.7205-0.22770.40250.8980.1692.0437-0.0496-0.04320.0770.06460.0580.11840.0505-0.00160.02120.11480.0030.01450.1739-0.00770.2931-18.360938.137-38.6775
181.34630.45670.11673.0886-0.03564.1939-0.1128-0.34610.06360.29510.11920.1116-0.3227-0.13720.00960.11280.01530.0410.196-0.00570.2281-16.223142.6535-31.1801
192.7599-0.70031.26142.68720.08582.7132-0.1716-0.24090.0760.16090.2131-0.1363-0.23790.04110.0170.119-0.01880.0350.20750.00330.2749-9.627343.148-37.9755
203.5744-0.4028-0.99971.14940.11950.9417-0.0379-0.03350.08650.08760.08030.3047-0.0311-0.19280.0210.14280.01020.03220.2190.02020.3562-23.3533.3639-36.587
210.7605-0.8977-0.44450.75830.15151.1325-0.0918-0.1231-0.0117-0.08190.0792-0.00390.10490.0779-0.00890.1284-0.02290.02930.1548-0.01280.2881-4.108330.4925-47.467
223.1781.56180.89867.0283.74084.59050.00440.3857-0.51820.093-0.0765-0.16860.9184-0.2102-0.05420.4238-0.01140.07360.2094-0.0250.2859-1.600610.3862-60.6341
232.16681.97850.91896.21494.17374.92020.01640.18730.0381-0.1372-0.29730.31530.1804-0.41570.49950.205-0.01390.00080.241-0.03050.3383-6.037324.6714-52.7907
241.95611.65660.91786.22843.51844.9604-0.0151-0.0306-0.09610.3026-0.16110.14710.6045-0.21820.1930.30430.00930.06920.2037-0.01040.2933-3.685516.7772-51.3676
254.56020.48711.45270.088-0.11434.4801-0.34610.31880.1697-0.8707-0.18960.84390.2528-0.220.42720.4299-0.0042-0.02120.2291-0.04750.2483-7.908118.4473-62.7813
264.19473.342.66186.64646.83389.8228-0.25540.1296-0.0526-1.286-0.01250.2074-0.40570.1240.24370.4701-0.01160.02860.24840.04770.2386-2.504121.3779-64.6603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 118 )A1 - 118
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 193 )A119 - 193
3X-RAY DIFFRACTION3chain 'A' and (resid 194 through 219 )A194 - 219
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 17 )B1 - 17
5X-RAY DIFFRACTION5chain 'B' and (resid 18 through 40 )B18 - 40
6X-RAY DIFFRACTION6chain 'B' and (resid 41 through 73 )B41 - 73
7X-RAY DIFFRACTION7chain 'B' and (resid 74 through 91 )B74 - 91
8X-RAY DIFFRACTION8chain 'B' and (resid 92 through 124 )B92 - 124
9X-RAY DIFFRACTION9chain 'B' and (resid 125 through 139 )B125 - 139
10X-RAY DIFFRACTION10chain 'B' and (resid 140 through 162 )B140 - 162
11X-RAY DIFFRACTION11chain 'B' and (resid 163 through 178 )B163 - 178
12X-RAY DIFFRACTION12chain 'B' and (resid 179 through 207 )B179 - 207
13X-RAY DIFFRACTION13chain 'B' and (resid 208 through 218 )B208 - 218
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 96 )C1 - 96
15X-RAY DIFFRACTION15chain 'C' and (resid 97 through 219 )C97 - 219
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 17 )D1 - 17
17X-RAY DIFFRACTION17chain 'D' and (resid 18 through 43 )D18 - 43
18X-RAY DIFFRACTION18chain 'D' and (resid 44 through 73 )D44 - 73
19X-RAY DIFFRACTION19chain 'D' and (resid 74 through 91 )D74 - 91
20X-RAY DIFFRACTION20chain 'D' and (resid 92 through 105 )D92 - 105
21X-RAY DIFFRACTION21chain 'D' and (resid 106 through 129 )D106 - 129
22X-RAY DIFFRACTION22chain 'D' and (resid 130 through 150 )D130 - 150
23X-RAY DIFFRACTION23chain 'D' and (resid 151 through 162 )D151 - 162
24X-RAY DIFFRACTION24chain 'D' and (resid 163 through 189 )D163 - 189
25X-RAY DIFFRACTION25chain 'D' and (resid 190 through 207 )D190 - 207
26X-RAY DIFFRACTION26chain 'D' and (resid 208 through 218 )D208 - 218

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