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- PDB-1t4k: Crystal Structure of Unliganded Aldolase Antibody 93F3 Fab -

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Basic information

Entry
Database: PDB / ID: 1t4k
TitleCrystal Structure of Unliganded Aldolase Antibody 93F3 Fab
Components
  • IMMUNOGLOBULIN IGG1, HEAVY CHAIN
  • IMMUNOGLOBULIN IGG1, KAPPA LIGHT CHAIN
KeywordsIMMUNE SYSTEM / enantioselectivity / aldolase antibody / reactive lysine / aldol reaction
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The Origin of Enantioselectivity in Aldolase Antibodies: Crystal Structure, Site-directed Mutagenesis, and Computational Analysis
Authors: Zhu, X. / Tanaka, F. / Hu, Y. / Heine, A. / Fuller, R. / Zhong, G. / Olson, A.J. / Lerner, R.A. / Barbas, C.F. / Wilson, I.A.
History
DepositionApr 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IMMUNOGLOBULIN IGG1, KAPPA LIGHT CHAIN
B: IMMUNOGLOBULIN IGG1, HEAVY CHAIN
C: IMMUNOGLOBULIN IGG1, KAPPA LIGHT CHAIN
D: IMMUNOGLOBULIN IGG1, HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,47113
Polymers93,8824
Non-polymers5899
Water4,990277
1
A: IMMUNOGLOBULIN IGG1, KAPPA LIGHT CHAIN
B: IMMUNOGLOBULIN IGG1, HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2687
Polymers46,9412
Non-polymers3275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-98 kcal/mol
Surface area19750 Å2
MethodPISA
2
C: IMMUNOGLOBULIN IGG1, KAPPA LIGHT CHAIN
D: IMMUNOGLOBULIN IGG1, HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2036
Polymers46,9412
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-127 kcal/mol
Surface area19760 Å2
MethodPISA
3
A: IMMUNOGLOBULIN IGG1, KAPPA LIGHT CHAIN
B: IMMUNOGLOBULIN IGG1, HEAVY CHAIN
hetero molecules

C: IMMUNOGLOBULIN IGG1, KAPPA LIGHT CHAIN
D: IMMUNOGLOBULIN IGG1, HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,47113
Polymers93,8824
Non-polymers5899
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area8920 Å2
ΔGint-313 kcal/mol
Surface area38230 Å2
MethodPISA
4
C: IMMUNOGLOBULIN IGG1, KAPPA LIGHT CHAIN
hetero molecules

B: IMMUNOGLOBULIN IGG1, HEAVY CHAIN
hetero molecules

A: IMMUNOGLOBULIN IGG1, KAPPA LIGHT CHAIN
D: IMMUNOGLOBULIN IGG1, HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,47113
Polymers93,8824
Non-polymers5899
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation3_545-x,y-1/2,-z+1/21
crystal symmetry operation3_555-x,y+1/2,-z+1/21
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-271 kcal/mol
Surface area43550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.701, 81.228, 149.496
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody IMMUNOGLOBULIN IGG1, KAPPA LIGHT CHAIN


Mass: 24100.611 Da / Num. of mol.: 2 / Fragment: antibody FAB 93f3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: 93f3 murine hybridoma
#2: Antibody IMMUNOGLOBULIN IGG1, HEAVY CHAIN


Mass: 22840.621 Da / Num. of mol.: 2 / Fragment: antibody FAB 93f3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: 93f3 murine hybridoma
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 298 K / pH: 5.5
Details: 16-20% (w/v) PEG 8000, 0.3 M zinc acetate, 0.1 M sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 1999
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 31622 / % possible obs: 91.3 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rsym value: 0.088 / Net I/σ(I): 17.4
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.43 / % possible all: 83.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FGW

2fgw


Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1370 -RANDOM
Rwork0.233 ---
obs0.233 30570 89.1 %-
all-30570 --
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6596 0 9 277 6882
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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