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- PDB-3gi8: Crystal Structure of ApcT K158A Transporter Bound to 7F11 Monoclo... -

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Basic information

Entry
Database: PDB / ID: 3gi8
TitleCrystal Structure of ApcT K158A Transporter Bound to 7F11 Monoclonal Fab Fragment
Components
  • 7F11 Anti-ApcT Monoclonal Fab Heavy Chain
  • 7F11 Anti-ApcT Monoclonal Fab Light Chain
  • Uncharacterized protein MJ0609
KeywordsTRANSPORT PROTEIN / membrane protein / transporter / antibody / Cell membrane / Membrane / Transmembrane / Structural Genomics / PSI-2 / Protein Structure Initiative / New York Consortium on Membrane Protein Structure / NYCOMPS
Function / homology
Function and homology information


transmembrane transporter activity / plasma membrane
Similarity search - Function
Amino acid/polyamine transporter I / Amino acid/polyamine transporter I / : / Amino acid/polyamine transporter I / Amino acid permease / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein MJ0609
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsShaffer, P.L. / Goehring, A.S. / Shankaranarayanan, A. / Gouaux, E. / New York Consortium on Membrane Protein Structure (NYCOMPS)
CitationJournal: Science / Year: 2009
Title: Structure and mechanism of a na+-independent amino Acid transporter.
Authors: Shaffer, P.L. / Goehring, A. / Shankaranarayanan, A. / Gouaux, E.
History
DepositionMar 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Uncharacterized protein MJ0609
L: 7F11 Anti-ApcT Monoclonal Fab Light Chain
H: 7F11 Anti-ApcT Monoclonal Fab Heavy Chain


Theoretical massNumber of molelcules
Total (without water)96,5423
Polymers96,5423
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-36 kcal/mol
Surface area35590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.039, 111.188, 115.674
Angle α, β, γ (deg.)90.00, 90.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein MJ0609


Mass: 48272.117 Da / Num. of mol.: 1 / Mutation: K158A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0609 / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q58026
#2: Antibody 7F11 Anti-ApcT Monoclonal Fab Light Chain


Mass: 24284.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Murine Hybridoma / Production host: Mus musculus (house mouse)
#3: Antibody 7F11 Anti-ApcT Monoclonal Fab Heavy Chain


Mass: 23984.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Murine Hybridoma / Production host: Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 3.07 Å3/Da / Density % sol: 59.89 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5
Details: 0.1M sodium acetate, 0.1M ammonium dihydrogen phosphate, 40-44% PEG 400, pH 5.0, Microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 24, 2008
RadiationMonochromator: Liquid Nitrogen cooled Dual Crystal/Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 36142 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 17.4
Reflection shellResolution: 2.59→2.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ApcT - Fab complex

Resolution: 2.59→50 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.867 / SU B: 12.891 / SU ML: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.685 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30685 1803 5 %RANDOM
Rwork0.25362 ---
obs0.25629 34311 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.772 Å2
Baniso -1Baniso -2Baniso -3
1--3.01 Å20 Å22.08 Å2
2--0.11 Å20 Å2
3---2.97 Å2
Refinement stepCycle: LAST / Resolution: 2.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6720 0 0 204 6924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226892
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9351.9559380
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2225871
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59523.944251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.569151107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8021516
X-RAY DIFFRACTIONr_chiral_restr0.0620.21087
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025094
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1730.23211
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.24843
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2351
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.223
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3361.54444
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.60927040
X-RAY DIFFRACTIONr_scbond_it0.46632817
X-RAY DIFFRACTIONr_scangle_it0.7734.52340
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.658 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 125 -
Rwork0.319 2431 -
obs--95.69 %

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