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- PDB-3fct: MATURE METAL CHELATASE CATALYTIC ANTIBODY WITH HAPTEN -

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Basic information

Entry
Database: PDB / ID: 3fct
TitleMATURE METAL CHELATASE CATALYTIC ANTIBODY WITH HAPTEN
Components(PROTEIN (METAL CHELATASE CATALYTIC ...) x 2
KeywordsIMMUNE SYSTEM / METAL CHELATASE / CATALYTIC ANTIBODY / FAB FRAGMENT
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / N-METHYLMESOPORPHYRIN
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRomesberg, F.E. / Santarsiero, B.D. / Barnes, D. / Yin, J. / Spiller, B. / Schultz, P.G. / Stevens, R.C.
CitationJournal: Biochemistry / Year: 1998
Title: Structural and kinetic evidence for strain in biological catalysis.
Authors: Romesberg, F.E. / Santarsiero, B.D. / Spiller, B. / Yin, J. / Barnes, D. / Schultz, P.G. / Stevens, R.C.
History
DepositionJun 13, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 22, 2020Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.4Sep 6, 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (METAL CHELATASE CATALYTIC ANTIBODY)
B: PROTEIN (METAL CHELATASE CATALYTIC ANTIBODY)
C: PROTEIN (METAL CHELATASE CATALYTIC ANTIBODY)
D: PROTEIN (METAL CHELATASE CATALYTIC ANTIBODY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,55716
Polymers93,0584
Non-polymers1,49912
Water9,836546
1
A: PROTEIN (METAL CHELATASE CATALYTIC ANTIBODY)
B: PROTEIN (METAL CHELATASE CATALYTIC ANTIBODY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3569
Polymers46,5292
Non-polymers8267
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PROTEIN (METAL CHELATASE CATALYTIC ANTIBODY)
D: PROTEIN (METAL CHELATASE CATALYTIC ANTIBODY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2027
Polymers46,5292
Non-polymers6735
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.290, 100.689, 73.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.768696, -0.044396, 0.638071), (-0.03005, -0.998993, -0.033307), (0.638908, 0.006428, -0.769256)-88.578, 82.7215, 139.7903
2given(0.753593, -0.005915, 0.657315), (-0.015668, -0.999837, 0.008965), (0.657155, -0.017055, -0.753563)-92.9298, 77.0969, 138.763
3given(0.757525, -0.058684, 0.650163), (-0.060283, -0.997984, -0.019841), (0.650017, -0.024163, -0.759536)-19.1128, 80.2548, 165.847
4given(0.763982, -0.061151, 0.642334), (-0.048339, -0.998126, -0.037528), (0.643425, -0.002379, -0.765506)-87.9134, 83.8807, 139.8223

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody PROTEIN (METAL CHELATASE CATALYTIC ANTIBODY)


Mass: 23432.014 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Details: CHIMERIC FAB FRAGMENT / Source: (gene. exp.) Homo sapiens (human) / Strain: SWISS WEBSTER / Cell: B LYMPHOCYTE / Cell line: 7G12 HYBRIDOMA / Cellular location: PERIPLASM / Organ: SPLEEN / Production host: Escherichia coli (E. coli)
#2: Antibody PROTEIN (METAL CHELATASE CATALYTIC ANTIBODY)


Mass: 23097.074 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Details: CHIMERIC FAB FRAGMENT / Source: (gene. exp.) Homo sapiens (human) / Strain: SWISS WEBSTER / Cell: B LYMPHOCYTE / Cell line: 7G12 HYBRIDOMA / Cellular location: PERIPLASM / Organ: SPLEEN / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 558 molecules

#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-MMP / N-METHYLMESOPORPHYRIN


Mass: 580.716 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H40N4O4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.6 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 27% PEG 2000-MME, 200 MM AMMONIUM SULFATE, 100 MM TRIS, PH 7.0, 10MM CADMIUM SULFATE, WITH 10-FOLD EXCESS OF DIASTEREOMERIC N- METHYLMESOPORPHYRIN AT 20C ...Details: PROTEIN WAS CRYSTALLIZED FROM 27% PEG 2000-MME, 200 MM AMMONIUM SULFATE, 100 MM TRIS, PH 7.0, 10MM CADMIUM SULFATE, WITH 10-FOLD EXCESS OF DIASTEREOMERIC N- METHYLMESOPORPHYRIN AT 20C (HANGING DROP)., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / % possible obs: 85.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HKL

1hkl


Resolution: 2.4→50 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1393 3.5 %RANDOM
Rwork0.206 ---
obs0.206 27726 69.9 %-
Solvent computationSolvent model: CNS / Bsol: 45.64 Å2 / ksol: 0.313 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6536 0 96 546 7178
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.51.5
X-RAY DIFFRACTIONc_mcangle_it5.52
X-RAY DIFFRACTIONc_scbond_it5.32
X-RAY DIFFRACTIONc_scangle_it7.12.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PACNS_TOPPAR:PROTEIN.TOP
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARACNS_TOPPAR:WATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4FCHEME.PARAMFCHEME.TOP

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