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- PDB-3gi9: Crystal Structure of ApcT Transporter Bound to 7F11 Monoclonal Fa... -

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Basic information

Entry
Database: PDB / ID: 3gi9
TitleCrystal Structure of ApcT 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 speciesMus musculus (house mouse)
Methanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.48 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 1.2Jun 7, 2017Group: Database references / Other
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,6003
Polymers96,6003
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-32 kcal/mol
Surface area34900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.365, 45.900, 158.088
Angle α, β, γ (deg.)90.00, 97.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: 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)
#2: 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)
#3: Protein Uncharacterized protein MJ0609


Mass: 48330.219 Da / Num. of mol.: 1
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5
Details: 0.1M sodium acetate, 0.1M rubidium chloride, 0.1M L-alanine, 40-48% PEG 400, pH 5.0, Microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2008
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: 2.48→50 Å / Num. obs: 36003 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 24.3
Reflection shellResolution: 2.48→2.59 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 2.1 / % possible all: 70.3

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.48→50 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.884 / SU B: 11.612 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.644 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29568 1819 5.1 %RANDOM
Rwork0.24792 ---
obs0.25033 34182 94.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.006 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-0.32 Å2
2--2.46 Å20 Å2
3----2.42 Å2
Refinement stepCycle: LAST / Resolution: 2.48→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6714 0 0 151 6865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226884
X-RAY DIFFRACTIONr_angle_refined_deg0.9371.9559364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8885868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52623.944251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.999151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9781516
X-RAY DIFFRACTIONr_chiral_restr0.0590.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025074
X-RAY DIFFRACTIONr_nbd_refined0.1690.23248
X-RAY DIFFRACTIONr_nbtor_refined0.2990.24829
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.29
X-RAY DIFFRACTIONr_mcbond_it0.3591.54454
X-RAY DIFFRACTIONr_mcangle_it0.54527020
X-RAY DIFFRACTIONr_scbond_it0.57832810
X-RAY DIFFRACTIONr_scangle_it0.7954.52344
LS refinement shellResolution: 2.48→2.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 104 -
Rwork0.312 1902 -
obs--71.36 %

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