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- PDB-4wbs: Crystal structure of an ABC transporter related protein from Burk... -

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Basic information

Entry
Database: PDB / ID: 4wbs
TitleCrystal structure of an ABC transporter related protein from Burkholderia phymatum
ComponentsABC transporter related
KeywordsTRANSPORT PROTEIN / SSGCID / ABC transporter / Burkholderia phymatum / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding
Similarity search - Function
LPS export ABC transporter, ATP-binding protein LptB / 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. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase ...LPS export ABC transporter, ATP-binding protein LptB / 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. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ABC transporter related
Similarity search - Component
Biological speciesBurkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of an ABC transporter related protein from Burkholderia phymatum
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Clifton, M.C. / Sankaran, B. / Lorimer, D. / Edwards, T.E.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter related
B: ABC transporter related
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2034
Polymers61,1322
Non-polymers712
Water5,188288
1
A: ABC transporter related
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6022
Polymers30,5661
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC transporter related
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6022
Polymers30,5661
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.070, 79.850, 121.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: CL / End label comp-ID: CL

Dom-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1chain AAA - C29 - 30037
2chain BBB - D16 - 30024

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Components

#1: Protein ABC transporter related


Mass: 30566.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia phymatum (bacteria) / Strain: DSM 17167 / STM815 / Gene: Bphy_0327 / Plasmid: BuphA.00057.b.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2JCQ1
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: JCSG-2, condition B5, optimized: 1M LiCl, 100mM Tris pH 8.5, 20% PEG 6000; cryo: 20% EDO; BuphA.00057.b.A1.PS01348 at 20mg/ml with 1mM ATP (invisible in electron density; tray 233360f3, puck wlt6-3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2012
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 36187 / Num. obs: 36187 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 29.54 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.073 / Χ2: 0.959 / Net I/σ(I): 16.05 / Num. measured all: 180799
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.055.10.8310.5863.1513537265526550.652100
2.05-2.110.8880.4593.9913019256225620.51100
2.11-2.170.9270.3594.9312779250525010.39999.8
2.17-2.240.9550.2935.9412359242124190.32699.9
2.24-2.310.9660.2397.1412008236023580.26699.9
2.31-2.390.9780.28.3511575228022790.222100
2.39-2.480.9820.1719.5411332223022280.1999.9
2.48-2.580.9880.13311.9110880214421420.14899.9
2.58-2.70.9890.11413.8610275203720340.12799.9
2.7-2.830.9940.0916.669889196319600.199.8
2.83-2.980.9950.07319.519390186818670.08299.9
2.98-3.160.9970.0623.28822177417710.06799.8
3.16-3.380.9970.0527.338280168216720.05699.4
3.38-3.650.9980.04331.097517155615500.04899.6
3.65-40.9980.03834.286911144614440.04399.9
4-4.470.9980.03635.356139132213170.0499.6
4.47-5.160.9980.03436.215442117611690.03899.4
5.16-6.320.9980.03335.02486410079970.03699
6.32-8.940.9990.03336.9137888077960.03798.6
8.940.9980.03338.2719934884660.03895.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
BALBESphasing
PHASERphasing
PHENIX(phenix.refine: dev_1779)refinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z47

1z47


Resolution: 2→44.771 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2373 2029 5.62 %
Rwork0.1831 34102 -
obs0.1862 36131 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.12 Å2 / Biso mean: 37.505 Å2 / Biso min: 14.66 Å2
Refinement stepCycle: final / Resolution: 2→44.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 2 288 3998
Biso mean--32.89 40.32 -
Num. residues----503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083781
X-RAY DIFFRACTIONf_angle_d1.1165144
X-RAY DIFFRACTIONf_chiral_restr0.044626
X-RAY DIFFRACTIONf_plane_restr0.005673
X-RAY DIFFRACTIONf_dihedral_angle_d12.5471386
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2080X-RAY DIFFRACTION8.27TORSIONAL
12B2080X-RAY DIFFRACTION8.27TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.31281550.246924012556100
2.05-2.10550.30621530.221823792532100
2.1055-2.16740.26541460.210724072553100
2.1674-2.23740.2631400.202524012541100
2.2374-2.31730.2611290.19824092538100
2.3173-2.41010.25581320.197924372569100
2.4101-2.51980.28381470.205623952542100
2.5198-2.65260.26091410.206524202561100
2.6526-2.81880.26721470.209324412588100
2.8188-3.03640.27051460.206324342580100
3.0364-3.34190.27531620.193324242586100
3.3419-3.82520.23771310.174824732604100
3.8252-4.81850.18281500.140424922642100
4.8185-44.78250.18281500.16082589273999
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)
13.4657-0.00160.09441.98391.87513.7142-0.0170.0420.0915-0.16640.1386-0.1181-0.00810.2348-0.1340.2-0.00780.01090.18990.05250.203533.405449.45399.8192
25.2571.1482-0.64462.797-1.27234.29550.1223-0.29930.5960.08070.17590.42010.054-0.3227-0.18880.21640.04620.01150.3724-0.01110.373121.713159.746131.7876
31.33420.6589-0.1061.83921.25851.2538-0.11210.20180.2804-0.29770.03740.3088-0.1207-0.0670.1130.2540.0129-0.05120.18450.06860.285117.182648.77788.4384
41.92571.97581.09942.48482.75246.66760.5815-0.7718-0.40490.07340.0246-0.26390.61910.206-0.72060.366-0.09450.03790.40230.01750.2187-9.671913.09515.7809
52.3771-0.83510.81634.1292-0.93052.4295-0.0438-0.5712-0.12830.47410.03060.3198-0.015-0.290.06890.1746-0.01970.04810.33330.00850.22884.24324.770730.8329
62.25080.2565-0.0343.0840.12682.6621-0.0520.1092-0.2618-0.35620.0206-0.04270.20330.18750.00540.1887-0.0047-0.01040.2074-0.03230.190412.460318.863913.3928
72.69760.09021.51766.96890.29537.9338-0.0919-0.16880.4599-0.4764-0.01761.2748-0.8829-0.3034-0.06390.29010.1001-0.02750.3422-0.08280.4525-3.937442.473418.2458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 111 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 187 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 188 through 274 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 16 through 30 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 31 through 99 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 100 through 252 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 253 through 274 )B0

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