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- PDB-2qrr: Crystal structure of the soluble domain of the ABC transporter, A... -

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Basic information

Entry
Database: PDB / ID: 2qrr
TitleCrystal structure of the soluble domain of the ABC transporter, ATP-binding protein from Vibrio parahaemolyticus
ComponentsMethionine import ATP-binding protein metN
KeywordsHYDROLASE / alpha-beta structure / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Amino-acid transport / ATP-binding / Inner membrane / Membrane / Nucleotide-binding / Transport
Function / homology
Function and homology information


ABC-type methionine transporter / ABC-type D-methionine transporter activity / Gram-negative-bacterium-type cell wall / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter, methionine import, ATP-binding protein MetN, proteobacteria / NIL domain / NIL domain / Methionine import ATP-binding protein metN family profile. / NIL / Methionine import ATP-binding protein MetN, ATP-binding domain / : / ACT domain / ACT-like domain / ABC transporter-like, conserved site ...ABC transporter, methionine import, ATP-binding protein MetN, proteobacteria / NIL domain / NIL domain / Methionine import ATP-binding protein metN family profile. / NIL / Methionine import ATP-binding protein MetN, ATP-binding domain / : / ACT domain / ACT-like domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Alpha-Beta Plaits / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Methionine import ATP-binding protein MetN
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.71 Å
AuthorsKim, Y. / Zhou, M. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Soluble Domain of the ABC Transporter, ATP-binding Protein from Vibrio parahaemolyticus.
Authors: Kim, Y. / Zhou, M. / Freeman, L. / Joachimiak, A.
History
DepositionJul 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 999 SEQUENCE AUTHORS CONFIRM THE PRESENCE OF ASN RESIDUE AT THE SEQUENCE POSITION 333 (RESIDUE NUMBER ... SEQUENCE AUTHORS CONFIRM THE PRESENCE OF ASN RESIDUE AT THE SEQUENCE POSITION 333 (RESIDUE NUMBER 87 IN COORDINATES) AND STATE THAT IT IS UNCLEAR WHETHER IT IS A MISTAKE FROM PCR OR A MISTAKE IN ORIGINAL SEQUENCING (IN SEQUENCE ANNOTATION IN THE UNIPROT DATABASE).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionine import ATP-binding protein metN
B: Methionine import ATP-binding protein metN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8183
Polymers22,7822
Non-polymers351
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.134, 47.780, 53.347
Angle α, β, γ (deg.)90.00, 118.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methionine import ATP-binding protein metN


Mass: 11391.136 Da / Num. of mol.: 2 / Fragment: Residues 247-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: metN, VP0706 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q87RS1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.4 M Ammonium phosphate dibasic, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2007 / Details: mirrors
RadiationMonochromator: double crystal, Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→46.88 Å / Num. all: 23458 / Num. obs: 23458 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.121 / Net I/σ(I): 10.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2186 / Rsym value: 0.365 / % possible all: 89.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXCDphasing
SHELXEmodel building
MLPHAREphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.71→46.88 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.153 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.124
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2383 10.2 %RANDOM
Rwork0.199 ---
all0.203 21072 --
obs0.203 21072 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.868 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20.31 Å2
2--0 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.71→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 1 128 1655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221632
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.681.9822222
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0125210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32425.42283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49815281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2321510
X-RAY DIFFRACTIONr_chiral_restr0.1240.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021288
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.2671
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21137
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2110
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.223
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4211.51054
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.84921656
X-RAY DIFFRACTIONr_scbond_it3.4043656
X-RAY DIFFRACTIONr_scangle_it4.8944.5566
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.71→1.754 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 126 -
Rwork0.205 1115 -
obs-1258 68.79 %
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)
11.05720.079-0.8641.7285-0.02031.10220.030.0675-0.062-0.0407-0.0899-0.0334-0.0018-0.04390.0599-0.0525-0.0013-0.0119-0.031-0.0112-0.009116.601413.50291.3356
20.344-0.1505-0.431.02520.25112.0790.0657-0.0222-0.02690.0211-0.12920.011-0.1924-0.14880.0635-0.02090.0243-0.024-0.0335-0.0055-0.0279.093125.153215.1683
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 985 - 101
2X-RAY DIFFRACTION2BB1 - 984 - 101

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