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- PDB-1uwg: Molecular Mechanism of Enantioselective Proton Transfer to Carbon... -

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Basic information

Entry
Database: PDB / ID: 1uwg
TitleMolecular Mechanism of Enantioselective Proton Transfer to Carbon in Catalytic Antibody 14D9
Components(ANTIBODY 14D9) x 2
KeywordsANTIBODY / CATALYTIC ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-KHA / PHOSPHATE ION
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsBaumann, U. / Reymond, J.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Molecular Mechanism of Enantioselective Proton Transfer to Carbon in Catalytic Antibody 14D9
Authors: Zheng, L. / Baumannn, U. / Reymond, J.L.
History
DepositionFeb 5, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 30, 2016Group: Derived calculations / Other
Revision 1.3Mar 15, 2017Group: Source and taxonomy
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: ANTIBODY 14D9
L: ANTIBODY 14D9
X: ANTIBODY 14D9
Y: ANTIBODY 14D9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,52912
Polymers94,4054
Non-polymers1,1258
Water1,53185
1
H: ANTIBODY 14D9
L: ANTIBODY 14D9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9558
Polymers47,2022
Non-polymers7526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
X: ANTIBODY 14D9
Y: ANTIBODY 14D9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5754
Polymers47,2022
Non-polymers3722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.470, 97.920, 70.880
Angle α, β, γ (deg.)90.00, 99.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21X
12H
22Y

NCS domain segments:

Refine code: 3

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLULYSLYSLB1 - 1071 - 107
211GLUGLULYSLYSXC1 - 1071 - 107
121ARGARGGLUGLULB108 - 213108 - 213
221ARGARGGLUGLUXC108 - 213108 - 213
112GLNGLNSERSERHA3 - 1153 - 119
212GLNGLNSERSERYD3 - 1153 - 119
122THRTHRLYSLYSHA116 - 214120 - 218
222THRTHRLYSLYSYD116 - 214120 - 218

NCS ensembles :
ID
1
2

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Components

#1: Antibody ANTIBODY 14D9


Mass: 23930.703 Da / Num. of mol.: 2 / Fragment: FAB HEAVY CHAIN, RESIDUES 1-221
Source method: isolated from a genetically manipulated source
Details: CATALYTIC ANTIBODY 19C9
Source: (gene. exp.) MUS MUSCULUS (house mouse), (gene. exp.) Homo sapiens (human)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10
#2: Antibody ANTIBODY 14D9


Mass: 23271.740 Da / Num. of mol.: 2 / Fragment: FAB LIGHT CHAIN, RESIDUES 1-213
Source method: isolated from a genetically manipulated source
Details: CATALYTIC ANTIBODY 19C9
Source: (gene. exp.) MUS MUSCULUS (house mouse), (gene. exp.) Homo sapiens (human)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10
#3: Chemical ChemComp-KHA / 1-(4-{[(2-HYDROXYETHYL)AMINO]CARBONYL}BENZYL)-1-METHYLPIPERIDINIUM


Mass: 277.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N2O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growpH: 8.5
Details: 45% MPD, 0.1 M TRIS, PH 8.5, 0.2 M AMMONIUM DIHYDROGEN PHOSPHATE,0.1M NAI
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
145 %(v/v)MPD1reservoir
20.2 Mmono ammonium dihydrogen phosphate1reservoir
30.1 MTris-HCl1reservoirpH8.5
416 mg/mlFab1drop
55 mM1dropNaCl
60.6 mMhapten 1a1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 2001 / Details: CONFOCAL MIRRORS
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.79→20 Å / Num. obs: 22991 / % possible obs: 99.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 0.375
Reflection shellResolution: 2.79→2.85 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.2 / % possible all: 85.8
Reflection
*PLUS
Highest resolution: 2.79 Å / Lowest resolution: 20 Å / Num. measured all: 85877 / Rmerge(I) obs: 0.137
Reflection shell
*PLUS
Lowest resolution: 2.96 Å / % possible obs: 97.2 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D5I

1d5i


Resolution: 2.79→20 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.809 / SU B: 17.09 / SU ML: 0.346 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1011 4.4 %RANDOM
Rwork0.204 ---
obs0.207 21887 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-0.74 Å2
2---1.11 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.79→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6344 0 70 85 6499
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0216574
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9548964
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0215836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.024954
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2850.22880
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.2249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5080.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.80.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6461.54194
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1181.56778
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1122380
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4144.52186
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1L852tight positional0.160.05
2H832tight positional0.170.05
1L785loose positional0.445
2H703loose positional0.535
1L852tight thermal0.270.5
2H832tight thermal0.260.5
1L785loose thermal1.7910
2H703loose thermal1.5110
LS refinement shellResolution: 2.79→2.86 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 26
Rwork0.258 1511
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)
10.11550.2462-1.11452.8688-1.12082.25940.09840.04950.07130.2626-0.0155-0.0018-0.25790.1529-0.08290.0989-0.0025-0.02810.119-0.01050.097115.62345.352640.3973
21.37890.17731.59352.73721.94488.2774-0.17140.19630.1491-0.2448-0.020.0656-0.42220.04620.19140.0436-0.01970.02960.080.03830.131523.201712.01884.1478
33.48340.36981.88022.42240.51894.9956-0.02320.02160.07440.01640.1186-0.00780.04590.3037-0.09550.0937-0.00410.04130.0468-0.0180.105616.0558-16.011332.8579
43.73190.96920.93634.11170.91832.0301-0.09040.3001-0.0255-0.21960.022-0.35220.16520.1520.06840.09740.04160.01180.1170.05650.041230.2126-1.786910.0582
50.56090.30140.27845.18351.48413.1901-0.0332-0.3937-0.00370.2181-0.0357-0.0030.1845-0.15940.06880.12630.04490.03090.16110.02620.13397.104425.924841.2748
62.61230.4916-0.53492.6223-4.225410.6619-0.04890.2259-0.1158-0.30940.004-0.20040.26520.03470.04490.1003-0.0029-0.0090.0469-0.04710.1185-0.305821.9634.5537
73.53020.7218-0.83254.2487-2.60317.302-0.1679-0.0801-0.10590.17130.0696-0.0372-0.4543-0.34430.09830.11320.0216-0.05840.1124-0.09560.21635.719447.703635.6058
81.4810.814-0.09954.138-0.6072.0057-0.08820.10560.0656-0.16490.07480.0684-0.1561-0.04650.01340.08840.04120.00490.1598-0.01410.08-8.335834.611.7396
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 109
2X-RAY DIFFRACTION2L110 - 213
3X-RAY DIFFRACTION3H4 - 113
4X-RAY DIFFRACTION4H114 - 215
5X-RAY DIFFRACTION5X1 - 109
6X-RAY DIFFRACTION6X110 - 213
7X-RAY DIFFRACTION7Y4 - 113
8X-RAY DIFFRACTION8Y114 - 215
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: r_bond_d / Dev ideal: 0.008

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