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- PDB-3nzh: Crystal structure of anti-emmprin antibody 5F6 FAB -

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Basic information

Entry
Database: PDB / ID: 3nzh
TitleCrystal structure of anti-emmprin antibody 5F6 FAB
Components
  • 5F6 HEAVY CHAIN
  • 5F6 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / immunoglobulin fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTeplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L.
CitationJournal: To be Published
Title: Crystal structure of anti-emmprin antibody 5F6 FAB
Authors: Teplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L.
History
DepositionJul 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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
L: 5F6 LIGHT CHAIN
H: 5F6 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2244
Polymers48,0732
Non-polymers1512
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-30 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.530, 129.740, 42.390
Angle α, β, γ (deg.)90.00, 109.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody 5F6 LIGHT CHAIN


Mass: 23573.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Mus musculus
Description: chimeric molecule, with mouse variable domain and human constant domain
Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody 5F6 HEAVY CHAIN


Mass: 24499.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Mus musculus
Description: chimeric molecule, with mouse variable domain and human constant domain
Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.61 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 8K, 0.1 M HEPES PH 7.5 CRYO CONDITIONS: 20% PEG 8K, 0.1 M HEPES PH 7.5, 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 8, 2008 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. all: 30870 / Num. obs: 30870 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.237 / Net I/σ(I): 4.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 1.8 / % possible all: 82

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0005refinement
d*TREK9.6Ldata reduction
d*TREK9.6Ldata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1NCA, 1PZ5

1nca

1pz5


Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.173 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.171 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24274 1258 4.1 %RANDOM
Rwork0.19541 ---
all0.19737 29609 --
obs0.19737 29609 89.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.171 Å0.191 Å
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 7 226 3561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223423
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.954657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6225434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.09924.519135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28115550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7561511
X-RAY DIFFRACTIONr_chiral_restr0.0970.2520
X-RAY DIFFRACTIONr_gen_planes_refined00.022571
X-RAY DIFFRACTIONr_nbd_refined0.2020.21453
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22316
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2254
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.216
X-RAY DIFFRACTIONr_mcbond_it2.74722226
X-RAY DIFFRACTIONr_mcangle_it4.34543515
X-RAY DIFFRACTIONr_scbond_it8.07781391
X-RAY DIFFRACTIONr_scangle_it9.89481142
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 71 -
Rwork0.235 1840 -
obs--82 %

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