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- PDB-3k4u: CRYSTAL STRUCTURE OF putative binding component of ABC transporte... -

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Basic information

Entry
Database: PDB / ID: 3k4u
TitleCRYSTAL STRUCTURE OF putative binding component of ABC transporter from Wolinella succinogenes DSM 1740 complexed with lysine
ComponentsBINDING COMPONENT OF ABC TRANSPORTER
KeywordsTRANSPORT PROTEIN / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / abc transporter / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / membrane
Similarity search - Function
Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LYSINE / BINDING COMPONENT OF ABC TRANSPORTER
Similarity search - Component
Biological speciesWolinella succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.62 Å
AuthorsMalashkevich, V.N. / Toro, R. / Morano, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF putative binding component of ABC transporter from Wolinella succinogenes DSM 1740 complexed with lysine
Authors: Malashkevich, V.N. / Toro, R. / Morano, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionOct 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 24, 2012Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: BINDING COMPONENT OF ABC TRANSPORTER
B: BINDING COMPONENT OF ABC TRANSPORTER
C: BINDING COMPONENT OF ABC TRANSPORTER
D: BINDING COMPONENT OF ABC TRANSPORTER
E: BINDING COMPONENT OF ABC TRANSPORTER
F: BINDING COMPONENT OF ABC TRANSPORTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,92712
Polymers170,0446
Non-polymers8836
Water2,090116
1
A: BINDING COMPONENT OF ABC TRANSPORTER
B: BINDING COMPONENT OF ABC TRANSPORTER
C: BINDING COMPONENT OF ABC TRANSPORTER
D: BINDING COMPONENT OF ABC TRANSPORTER
E: BINDING COMPONENT OF ABC TRANSPORTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,43910
Polymers141,7035
Non-polymers7365
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-14 kcal/mol
Surface area31500 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-13 kcal/mol
Surface area31450 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.406, 149.151, 81.969
Angle α, β, γ (deg.)90.00, 100.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BINDING COMPONENT OF ABC TRANSPORTER


Mass: 28340.605 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolinella succinogenes (bacteria) / Strain: DSM 1740 / Gene: CAE09431.1, WS0279 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q7MAG0
#2: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.79 Å3/Da / Density % sol: 55.95 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 10% iso-propanol, 0.1 M Hepes, 20% PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 12.01 / Number: 377460 / Rmerge(I) obs: 0.124 / Χ2: 1.66 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 100715 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.325099.510.0493.4963.8
5.817.3299.610.0752.6513.6
5.085.8199.810.0822.5093.8
4.625.0810010.0732.6013.8
4.294.6299.910.0812.3143.8
4.034.2999.910.0961.9823.8
3.834.0399.910.1121.7713.9
3.663.8310010.1441.4753.9
3.523.6610010.1681.4213.9
3.43.5210010.2021.2783.9
3.33.410010.2691.1843.9
3.23.310010.3411.1423.9
3.123.210010.4471.1463.9
3.043.1210010.5521.1433.9
2.973.0410010.5951.1563.8
2.912.9710010.6751.1473.8
2.852.9199.910.9081.1363.7
2.82.8599.111.1743.5
2.752.897.111.1883.3
2.72.7592.311.1243.1
ReflectionResolution: 2.62→50 Å / Num. obs: 100715 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 7
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.1 % / % possible all: 92.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMAC5.5.0089refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.62→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.904 / Occupancy max: 1 / Occupancy min: 1 / SU B: 28.98 / SU ML: 0.251 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2657 5.2 %RANDOM
Rwork0.202 ---
obs0.205 51195 90.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.41 Å2
Baniso -1Baniso -2Baniso -3
1--5.47 Å20 Å2-6.33 Å2
2---4.14 Å20 Å2
3---9.61 Å2
Refinement stepCycle: LAST / Resolution: 2.62→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11238 0 60 116 11414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211550
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.97715572
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.27251393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27624.762504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.314152149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.3411542
X-RAY DIFFRACTIONr_chiral_restr0.1220.21699
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218536
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0823.56959
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.8115011186
X-RAY DIFFRACTIONr_scbond_it11.276504591
X-RAY DIFFRACTIONr_scangle_it1.0334.54386
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.75 Å / Total num. of bins used: 20
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)
11.11550.0622-0.18580.72930.0972.1875-0.08290.22560.1424-0.18640.00290.153-0.0757-0.03740.08010.5121-0.006-0.08860.39490.01690.0539-6.6197-9.4601-11.7418
21.2152-0.36840.55662.5829-0.69811.3855-0.00840.0421-0.2469-0.1026-0.0841-0.23620.16820.04990.09250.34780.03340.07480.3193-0.01680.114617.4003-34.1748.9035
30.62690.2323-0.17392.61560.74570.79110.0576-0.08920.01970.2466-0.05490.1664-0.0881-0.0436-0.00270.41990.00080.01890.334-0.03250.0196-18.2534-51.8281-7.1056
41.38890.0126-0.59821.096-0.08232.11970.10970.09220.0863-0.2086-0.1088-0.2631-0.26250.0368-0.00090.3889-0.01470.03270.26010.04120.07084.7276-59.0032-39.1977
52.903-0.1368-0.68681.201-0.07421.2164-0.10860.0021-0.05440.06410.02890.09380.0965-0.16620.07960.4143-0.0069-0.00550.3952-0.03410.0157-18.9286-23.581123.8343
63.07370.50910.57241.8191-0.37930.6052-0.09090.27110.2235-0.15850.02760.26690.0181-0.15150.06330.3649-0.0117-0.05440.4485-0.03190.0678-31.6889-75.84-36.4673
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 233
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION1A502 - 523
4X-RAY DIFFRACTION2B1 - 233
5X-RAY DIFFRACTION2B501
6X-RAY DIFFRACTION2B502 - 520
7X-RAY DIFFRACTION3C1 - 233
8X-RAY DIFFRACTION3C501
9X-RAY DIFFRACTION3C502 - 520
10X-RAY DIFFRACTION4D1 - 233
11X-RAY DIFFRACTION4D501
12X-RAY DIFFRACTION4D502 - 518
13X-RAY DIFFRACTION5E0 - 233
14X-RAY DIFFRACTION5E501
15X-RAY DIFFRACTION5E502 - 523
16X-RAY DIFFRACTION6F1 - 233
17X-RAY DIFFRACTION6F501
18X-RAY DIFFRACTION6F502 - 518

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