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- PDB-4hul: MATE transporter NorM-NG in complex with Cs+ and monobody -

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Basic information

Entry
Database: PDB / ID: 4hul
TitleMATE transporter NorM-NG in complex with Cs+ and monobody
Components
  • Multidrug efflux protein
  • Protein B
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


cell-substrate junction assembly / proteoglycan binding / extracellular matrix structural constituent / cell-matrix adhesion / integrin binding
Similarity search - Function
: / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesNeisseria gonorrhoeae (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.81 Å
AuthorsLu, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures of a Na+-coupled, substrate-bound MATE multidrug transporter.
Authors: Lu, M. / Symersky, J. / Radchenko, M. / Koide, A. / Guo, Y. / Nie, R. / Koide, S.
History
DepositionNov 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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
A: Multidrug efflux protein
B: Protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7673
Polymers60,6352
Non-polymers1331
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.334, 118.334, 227.322
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Multidrug efflux protein


Mass: 49717.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: NGTW08_0430 / Production host: Escherichia coli (E. coli) / References: UniProt: E8SM44
#2: Protein Protein B


Mass: 10916.989 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: M1E1G6*PLUS
#3: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cs

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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: 7.57 Å3/Da / Density % sol: 83.76 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 8 / Details: PEG, pH 8, VAPOR DIFFUSION, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jan 1, 2010
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→60 Å / Num. all: 20000 / Num. obs: 18316 / % possible obs: 98.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.81→20 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.866 / SU B: 130.775 / SU ML: 0.779 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 3.495 / ESU R Free: 0.721 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.37553 933 5.1 %RANDOM
Rwork0.31081 ---
all0.3 20000 --
obs0.31387 17371 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 159.779 Å2
Baniso -1Baniso -2Baniso -3
1-6.25 Å23.13 Å20 Å2
2--6.25 Å20 Å2
3----9.38 Å2
Refinement stepCycle: LAST / Resolution: 3.81→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4215 0 1 0 4216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.024334
X-RAY DIFFRACTIONr_bond_other_d00.022864
X-RAY DIFFRACTIONr_angle_refined_deg2.3411.9535902
X-RAY DIFFRACTIONr_angle_other_deg4.69136946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.5045548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23421.788151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.58915658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0251520
X-RAY DIFFRACTIONr_chiral_restr0.1310.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214802
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02998
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.81→3.905 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.524 51 -
Rwork0.531 1036 -
obs--90.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.69690.10470.92140.3890.54741.81430.01120.3252-0.1169-0.08420.03420.0562-0.17170.2639-0.04540.0467-0.0942-0.02260.47170.00450.10767.4607-49.318626.949
22.8624-2.67760.16764.2634-2.08013.3189-0.171-0.4113-0.1034-0.04170.1810.03870.10360.656-0.010.04450.0143-0.00530.3531-0.01860.1667-32.1204-59.99728.6444
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 463
2X-RAY DIFFRACTION2B1 - 91

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